ggbio - grammar of graphics for genomic data

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