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Citation preview
Reproducible reports with Markdown knitr
Mikhail Dozmorov
Summer 2018
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 1 58
Literate programming
Let us change our traditional attitude to the construction of programsInstead of imagining that our main task is to instruct a computer what todo let us concentrate rather on explaining to humans what we wantthe computer to do
ndash Donald E Knuth Literate Programming 1984
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 2 58
Name to know Edward TufteldquoDesign cannot rescue failed contentrdquo
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 3 58
Tuftersquos Rules
1 Show the data2 ldquoInduce the viewer to think about the substance rather than about
methodology graphic design the tech of graphic production orsomething elserdquo
3 Avoid Distorting the Data4 Present Many Numbers in a Small Space5 Make Large Datasets Coherent6 Encourage Eyes to Compare Data7 Reveal Data at Several Levels of Detail8 Serve a Reasonably Clear Purpose9 Be Closely Integrated with Statistical and Verbal Descriptions of the
Dataset
httpwwwsealthreinholdcomschooltuftes-rulesrule_onephp
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 4 58
Document formatting
Document formatting
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 5 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Literate programming
Let us change our traditional attitude to the construction of programsInstead of imagining that our main task is to instruct a computer what todo let us concentrate rather on explaining to humans what we wantthe computer to do
ndash Donald E Knuth Literate Programming 1984
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 2 58
Name to know Edward TufteldquoDesign cannot rescue failed contentrdquo
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 3 58
Tuftersquos Rules
1 Show the data2 ldquoInduce the viewer to think about the substance rather than about
methodology graphic design the tech of graphic production orsomething elserdquo
3 Avoid Distorting the Data4 Present Many Numbers in a Small Space5 Make Large Datasets Coherent6 Encourage Eyes to Compare Data7 Reveal Data at Several Levels of Detail8 Serve a Reasonably Clear Purpose9 Be Closely Integrated with Statistical and Verbal Descriptions of the
Dataset
httpwwwsealthreinholdcomschooltuftes-rulesrule_onephp
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 4 58
Document formatting
Document formatting
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 5 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Name to know Edward TufteldquoDesign cannot rescue failed contentrdquo
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 3 58
Tuftersquos Rules
1 Show the data2 ldquoInduce the viewer to think about the substance rather than about
methodology graphic design the tech of graphic production orsomething elserdquo
3 Avoid Distorting the Data4 Present Many Numbers in a Small Space5 Make Large Datasets Coherent6 Encourage Eyes to Compare Data7 Reveal Data at Several Levels of Detail8 Serve a Reasonably Clear Purpose9 Be Closely Integrated with Statistical and Verbal Descriptions of the
Dataset
httpwwwsealthreinholdcomschooltuftes-rulesrule_onephp
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 4 58
Document formatting
Document formatting
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 5 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Tuftersquos Rules
1 Show the data2 ldquoInduce the viewer to think about the substance rather than about
methodology graphic design the tech of graphic production orsomething elserdquo
3 Avoid Distorting the Data4 Present Many Numbers in a Small Space5 Make Large Datasets Coherent6 Encourage Eyes to Compare Data7 Reveal Data at Several Levels of Detail8 Serve a Reasonably Clear Purpose9 Be Closely Integrated with Statistical and Verbal Descriptions of the
Dataset
httpwwwsealthreinholdcomschooltuftes-rulesrule_onephp
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 4 58
Document formatting
Document formatting
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 5 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Document formatting
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 5 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Writing reports
HTML - HyperText Markup Language used to create web pagesDeveloped in 1993LaTeX ndash a typesetting system for production of technicalscientificdocumentation PDF output Developed in 1994Sweave ndash a tool that allows embedding of the R code in LaTeXdocuments PDF output Developed in 2002Markdown ndash a lightweight markup language for plain text formattingsyntax Easily converted to HTML
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 6 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
HTML example
HTML files have htm or html extensionsPairs of tags define contentformatting
lth1gt Header level 1 lth1gtlta href=ldquohttpwwwrdquogt Link ltagtltpgt Paragraph ltpgt
ltDOCTYPE htmlgtlthtmlgtltheadgtltmeta http-equiv=Content-Type content=texthtml charset=utf-8gtltheadgt
ltbodygtlth1gtMarkdown examplelth1gt
ltpgtThis is a simple example of a Markdown documentltpgt
You can emphasize code with ltstronggtboldltstronggt or ltemgtitalicsltemgt or ltcodegtmonospaceltcodegt fontltbodygtlthtmlgt
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 7 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
LaTeX example
LaTeX files usually have a tex extensionLaTeX commands define appearance of text and other formattingstructures
documentclassarticleusepackagegraphicx
begindocument
titleIntroduction to LaTeXauthorAuthors Name
maketitle
beginabstractThis is abstract text This simple document shows very basic features ofLaTeXendabstract
sectionIntroductionhttpwwwelectronicsoulufilatexexamplesexample_1
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 8 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Sweave example
Sweave files typically have an Rnw extensionLaTeX syntax for text ltltchunk_namegtgt= ltcodegt syntax outlinescode blocks
documentclassarticle
usepackageamsmath
usepackagenatbibusepackageindentfirst
DeclareMathOperatorlogitlogit
VignetteIndexEntryLogit-Normal GLMM Examples
begindocument
First we attach the dataltltboothgtgt=library(bernor)data(booth)attach(booth)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 9 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Markdown
Markdown is a markup language like HTML and LaTeX but designedto be as lightweight as possibleThe goal is still to separate form and content but also to prioritizehuman-readability even at the cost of fancy featuresYou can learn Markdown in about 5 minutes If you can write an emailyou can write MarkdownOr use a desktop Markdown editor like MarkdownPad (Windows) orMacDown (Mac)
httpbioconnectorgithubiomarkdown
httpmarkdownpadcom
httpmacdownuranusjrcom
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 10 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Basic Markdown Syntax
Regardless of your chosen output format some basic syntax will be useful
Section headersText emphasisListsR code
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 11 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Section Headers
To set up different sized header text in your document use for Header 1 for Header 2 and for Header 3
In a presentation this creates a new slide
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 12 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Text emphasis
Italicize text via Italicize or _Italicize_Bold text via Bold or __Bold__
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 13 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Unordered Lists
This code
Item 1 Item 2
+ Item 2a+ Item 2b
Renders these bullets (sub-lists need 1 tab or 4 spaces)
Item 1Item 2
Item 2aItem 2b
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 14 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Ordered ListsThis code
1 Item 12 Item 2
+ Item 2a+ Item 2b
Renders this list (be advised - the bullets may not look great in alltemplates)
1 Item 12 Item 2
Item 2aItem 2bMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 15 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Inline R Code
To use R within a line use the syntax wrapped in single forward ticksr dim(mtx)This can be useful to refer to estimates confidence intervals p-valuesetc in the body of an articlehomework without worrying about copyerrors
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 16 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Markdown syntax
superscript^2^~~strikethrough~~
Linkshttpexamplecom[linked phrase](httpexamplecom)
Images[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
BlockquotesA friend once saidgt Its always better to givegt than to receive
Horizontal Rule Page Break------
Tables
First Header | Second Header------------- | -------------Content Cell | Content CellContent Cell | Content Cell
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 17 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Large code chunks
Marked with triple backticks
```r optionalChunkName echo=TRUE results=hide R code here```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 18 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Creating R markdown document
Regular text file with Rmd extensionCreate manually or use RStudio
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 19 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
YAML header (think settings)
YAML - YAML Ainrsquot Markup LanguageYAML is a simple text-based format for specifying data like JSON
---title Untitledauthor rdquoYour Namedate rdquoCurrent dateoutput html_document---
output is the critical part ndash it defines the output format Can bepdf_document or word_documenthttpsgithubcommdozmorovMDmisc
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 20 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
YAML header for a PDF presentation
---title Reproducible reports with Markdown knitrauthor Mikhail Dozmorovdate Summer 2018outputbeamer_presentation colortheme seahorsecolortheme dolphinfig_caption nofig_height 6fig_width 7fonttheme structurebold theme boxestheme AnnArbor
---Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 21 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
YAML header for a Word document
---bibliography [3D_refsbibbrainbib]csl stylesrefgenomebiologycsloutputword_documentreference_docx stylesdocNIH_grant_styledocx
pdf_document defaulthtml_document default
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 22 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Modifying the behavior of R code chunksChunk options comma-separated
echo=FALSE - hides the code but not the resultsoutput DefaultTRUEresults=lsquohidersquo - hides the resultsoutput markup (the default)takes the result of the R evaluation and turns it into markdown that isrendered as usual hold ndash hold will hold all the output pieces andpush them to the end of a chunk Useful if yoursquore running commandsthat result in lots of little pieces of output in the same chunk hidewill hide results asis writes the raw results from R directly into thedocument Only really useful for tableseval=FALSE - disables code execution Default TRUEcache=TRUE - turn on caching of calculation-intensive chunk DefaultFALSEfigwidth= figheight= - customize the size of a figuregenerated by the code chunkinclude (TRUE by default) if this is set to FALSE the R code is stillevaluated but neither the code nor the results are returned in theoutput document
The full list of options httpyihuinameknitroptions
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 23 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Global chunk options
Some options you would like to set globally instead of typing them foreach chunk
knitropts_chunk$set(figwidth=12 figheight=8 figpath=imgrsquo cachepath=cache cache=FALSE echo=FALSE warning=FALSE message=FALSE)
warning=FALSE and message=FALSE suppress any R warnings ormessages from being included in the final documentfigpath=img - the figure files get placed in the img subdirectory(Default not saved at all)
A special note about caching The cache= option is automatically set toFALSE That is every time you render the Rmd all the R code is run againfrom scratch If you use cache=TRUE for this chunk knitr will save theresults of the evaluation into a directory that you specify egcachepath=cache When you re-render the document knitr willfirst check if there are previously cached results under the cache directorybefore really evaluating the chunk if cached results exist and this codechunk has not been changed since last run (use MD5 sum to verify) thecached results will be (lazy-) loaded otherwise new cache will be built if acached chunk depends on other chunks (see the dependson option) andany one of these chunks has changed this chunk must be forcibly updated(old cache will be purged) See the documentation for caching
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 24 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
An example of R Markdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 25 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
KnitR
KnitR ndash Elegant flexible and fast dynamic report generation writtenin R Markdown PDF HTML DOCX output Developed in 2012
installpackages(knitr dependencies = TRUE)
httpsgithubcomyihuiknitr httpyihuinameknitr
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 26 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Displaying data as tables
KnitR has built-in function to display a table
data(mtcars)knitrkable(head(mtcars))
pander package allows more customization
panderpander(head(mtcars))
xtable package has even more options
xtablextable(head(mtcars))
DT package an R interface to the DataTables library
DTdatatable(mtcars)httpbioconnectorgithubiomarkdownrmarkdownmdPrinting_tables_nicely
httpscranr-projectorgwebpackagesxtablevignettesxtableGallerypdf
httpscranr-projectorgwebpackageskableExtravignettesawesome_table_in_htmlhtml
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 27 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Including figures
Plots may be generated by R code and displayed in the outputdocumentExisting image files like jpg png may be inserted like
[](httpexamplecomlogopng)[optional caption text](figuresimgpng)
Alternatively use knitr capabilitiesr outwidth = 300px echo=FALSEknitrinclude_graphics(imgbandThree2png)For PDF output use LaTeX syntax
begincenterincludegraphics[height=170px]imgbioinfo3pngendcenter
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 28 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Customizing Figures Captions
The figcap option allows you to specify the caption for the figuregenerated by a given chunk
```r caption figcap=I am the captionplot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 29 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Customizing Figures Size
The figheight and figwidth options let you specify the dimensions ofyour plots
```r caption figheight = 4 figwidth = 8plot(pressure)```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 30 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Creating the final report
Markdown documents (md or Rmd) can be converted to HTMLusing markdownmarkdownToHTML(markdown_examplemdmarkdown_examplehtml)Another option is to usermarkdownrender(markdown_examplemdrsquo) At the backend ituses pandoc command line tool installed with RstudioRstudio ndash one button knit2html() knit2pdf() functions
Note KnitR compiles the document in an R environment separate fromyours (think Makefile) Do not use Rprofile file - it loads into yourenvironment onlyhttppandocorg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 31 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Things to include in your final report
setseed(12345) ndash initialize random number generator
Include session_info() at the end ndash outputs all packagesversions used
```r sessionInfodiagnostics lt- devtoolssession_info()platform lt- dataframe(diagnostics$platform gt unlist stringsAsFactors = FALSE)colnames(platform) lt- c(description)pander(platform)packages lt- asdataframe(diagnostics$packages)pander(packages[ packages$`` == ])```
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 32 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Making default RMarkdown document on your own
Altering the default Rmarkdown file each time you write a homeworkreport or article would be a pain
Fortunately you donrsquot have to
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 33 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Templates
You can create your own templates which set-up packages fonts defaultchunk options etc
httprmarkdownrstudiocomdeveloper_document_templateshtmlSome packages (eg rticles) provide templates that meet journalrequirements or provide other
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 34 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Document formatting
Parameters
You may also set parameters in your documentrsquos YAML header
---output html_documentparamsdate 2017-11-02
---
or pass new values with the render function
This creates a read-only list params containing the values declaredeg params$date returns 2017-11-02
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 35 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
Bibliography
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 36 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
BibTex
articleBerkum2010aaAbstract = The three-dimensional folding of chromosomes Author = van Berkum Nynke L and Lieberman-Aiden Erez and Williams Louise and Imakaev Maxim and Gnirke Andreas and Mirny Leonid A and Dekker Job and Lander Eric SDate-Added = 2016-10-08 142623 +0000Date-Modified = 2016-10-08 142623 +0000Doi = 1037911869Journal = J Vis ExpJournal-Full = Journal of visualized experiments JoVEMesh = Chromosome Positioning Chromosomes DNA Genomics Nucleic Acid ConformationNumber = 39Pmc = PMC3149993Pmid = 20461051Pst = epublishTitle = Hi-C a method to study the three-dimensional architecture of genomesYear = 2010Bdsk-Url-1 = httpdxdoiorg1037911869Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 37 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
BibTex managers
JabRef for Windows httpwwwjabreforgBibDesk for Mac httpbibdesksourceforgenet
Save references in bib text file
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 38 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
Convert anything to BibTex
doi2bib - BibTex from DOI arXiv biorXiv httpswwwdoi2biborgZoteroBib - create a bibliography from a URL ISBN DOI PMIDarXiv ID or title Download as BibTex and more httpszbiborg
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 39 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
BibTex and RMarkdown
Add to YAML header
bibliography 3D_refsbib
Insert into RMarkdown as
The 3D structure of the human genome has proven to be highly organized[Dixon2012aa Rao2014aa] This organization starts from distinctchromosome territories [Cremer2010aa] following by topologically associateddomains (TADs) [Dixon2012aa Jackson1998aa Ma1998aa Nora2012aa Sexton2012aa]smaller sub-TADs [Phillips-Cremins2013aa Rao2014aa] and on themost local level individual regions of interacting chromatin [Rao2014aa Dowen2014aa Ji2016aa]
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 40 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
Format your BibTex references
Add to YAML header
csl genomebiologycsl
Get more styles at httpswwwzoteroorgstyles
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 41 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Bibliography
Format your Word output
If knitting into Word output you may want to have fonts headersmargins other than defaultCreate a Word document with the desired formatting Change fontstyles by right-clicking on the font (eg ldquoNormalrdquo) and select ldquoModifyrdquoInclude it into YAML header
outputword_documentreference_docx stylesdocNIH_grant_styledocx
httpsgithubcommdozmorovpresentationstreemasterioslides_template
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 42 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Math formulas
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 43 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Markdown Code MathJax
Markdown supports MathJax JavaScript engine to rendermathematical equations and formulasInline equations - use single ldquodollar signrdquo $ to specify MathJax coding
$s^2 = fracsum(x-barx)^2n-1$
s2 =sum
(xminusx)2nminus1
Check out this online tutorial httpmetamathstackexchangecomquestions5020mathjax-basic-tutorial-and-quick-reference
httpsgithubcomohsu-knight-cancer-biostatisticsreproducible-researchblob32bba6a78e347d64745982fb6245915cecb1b7c3slides-info-reproducible-researchstudy-group-2016Chpt201320Web20PresentationsMathJax_2Rmd
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 44 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Centering you equations
Insertion of two dollar signs $$ centers your equations Other examples offset and centered - notice double dollar signs
$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $
$$ sum_i=0^n i^2 = frac(n^2+n)(2n+1)6 $$
Inline equationsumn
i=0 i2 = (n2+n)(2n+1)6 on the same line Or self-standing
equation on a separate linensum
i=0i2 = (n2 + n)(2n + 1)
6
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 45 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
More Interesting Codes
Greek Letters
$alpha$ $beta$ $gamma$ $chi$$Delta$ $Sigma$ $Omega$
Greek Letters (not all capitalized Greek letters available)
α β γ χ
∆ Σ Ω
superscripts (ˆ) and subscripts (_)
x2i log2x
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 46 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Grouping with Brackets
Use brackets to delimit a formula containing a superscript orsubscript Notice the difference the grouping makes
$x^y^z$$x^y^z$$x_i^2$$x_i^2$
xy z xy z x2i xi2
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 47 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Scaling
Add the scaling code left(right) to make automatic sizeadjustments
$(fracsqrt xy^3)$$left(fracsqrt xy^3right)$
(radic
xy3 )
(radicx
y3
)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 48 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Sums and Integrals
Subscript (_) designates the lower limit superscript (ˆ) designates upperlimit
$sum_1^n$ $sum_i=0^infty i^2$
sumn1suminfin
i=0 i2
Other notable symbols
- $prod$ $infty$- $bigcup$ $bigcap$- $int$ $iint$
prodinfin⋃ ⋂ int intintMikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 49 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Radical Signs
Use lsquosqrtrsquo code to adjust the size of its argument Note the change in sizeof the square root function based on the code
1 $sqrtx^3$2 $sqrt[3]frac xy$and for complicated expressions use brackets
3 $^12$
1radic
x3
2 3radic
xy
3 12
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 50 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
You can also change fonts
$mathbb or $Bbb for Blackboard bold$mathbf for boldface$mathtt for typewritter font$mathrm for roman font$mathsf for sans-serif$mathcal for caligraphy$mathscr for script letter$mathfrak for Fraktur (old German style)
ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG ABCDEFG
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 51 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
You can also change fonts
Some special functions such as ldquolimrdquo ldquosinrdquo ldquomaxrdquo and ldquolnrdquo are normally setin roman font instead of italic Use lim sin to make these (roman)
$sin x$ (roman) vs $sin x$ (italics)
sin x (roman) vs sinx (italics)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 52 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
And add curly brackets
$$begincaseswidehatIF_1D = IF_1D - f(D)2 widehatIF_2D = IF_2D + f(D)2endcases (1)$$
IF1D = IF1D minus f (D)2IF2D = IF2D + f (D)2(1)
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 53 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
RStudio bonusInline preview of forumlas and images in an RMarkdown document
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 54 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
LATEX and Markdown
Rendering Markdown as a pdf requires a LATEX installationYou will additionally need to install Pandoc from httppandocorgWith LATEX many customizations are possible
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 55 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
LATEX Customization 1
You can include additional LATEX commands and contentUse the includes option as follows to add your favorite style files forthe preamble titleabstract bibliography etc
---title A More Organized Persons Documentoutputbeamer_presentationincludesin_header headertexbefore_body doc_prefixtexafter_body doc_suffixtex
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 56 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
LATEX Customization 2
If you prefer a self-contained document you may opt for theheader-includes option over the modular approach
---title BIOST 691 Reproducible Research Toolsauthor Author Namedate November 2 2017header-includes
- usepackagegraphicxoutputbeamer_presentationtheme Frankfurt
---
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 57 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
Math formulas
Note LATEXin Text
In Markdown ldquoLaTeX rocksrdquo renders as ldquoLATEXrocksrdquo (no space)Use ldquoLaTeX rocksrdquo to render ldquoLATEX rocksrdquo insteadThis can be especially important when using new commands
Mikhail Dozmorov Reproducible reports with Markdown knitr Summer 2018 58 58
![arXiv:1402.1894v1 [stat.OT] 8 Feb 2014 · phisticated. R Markdown is a new technology that makes creating fully-reproducible statistical analysis simple and painless. It provides](https://img.dokumen.tips/doc/110x75/5e1817c4f8163b6b672c2255/arxiv14021894v1-statot-8-feb-2014-phisticated-r-markdown-is-a-new-technology.jpg)
![Markdown Slides [EN]](https://img.dokumen.tips/doc/110x75/5584ef5ed8b42a73618b4c7d/markdown-slides-en.jpg)
