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Stefan Wyder
27. March 12
GGbio - grammar of graphics
for genomic data
What is ggplot2 A high-level R package for creating statistical graphics
also for summarizing and transforming data
inspired by „The Grammar of Graphics“Leland Wikinson 1999
INTERACTIVE!! Build plots iteratively and edit them later
Minimize the code needed
Build your new types of display
ggplot – even more functionality
ggplot(aes(carat, price), data=diamonds) + geom_point() + facet_grid(color ~ .)
ggplot(aes(carat, price, col=color), data=diamonds) + ylab("dollars") + xlim(c(0,2)) + geom_point()
Geom
Facet
x y
What is GGbio
• Extension and specialization of ggplot2
• for data types often used with genomic high-throughput data(Sequence data, Annotation, Chromosome PlotsGWAS/Manhattan Plot)
horizontal axis: genomic coordinatesFacets: chromosome or chromosome regions
• progressing fast, documentation not always updated – check regularly
Data Structure>library(ggplot2)>library(ggbio)
Functions
Example 1 – Seq data
Example 1 – Faceting
Example 2 – Annotation
Example 3
More info
http://tengfei.github.com/ggbio/
Installation
source("http://bioconductor.org/biocLite.R")biocLite("ggbio")
Future of Ggplot2
• see Webinar by Hadley (who wrote Ggplot2)
www.revolutionanalytics.com/news-events/free-webinars/2012/ggplot2-with-hadley-wickham
• making it faster• Maps