rainfall: produce an embellished rainfall plot using TCGA mutation data

In genomicsclass/ph525x: support functions and data for edX course PH525

produce an embellished rainfall plot using TCGA mutation data

Description

produce an embellished rainfall plot using TCGA mutation data

Usage

rainfall(mut, colmap = kataColors(), oind = 1, 
   ptcex = 0.1, dodensity = TRUE, inbw = 1000, 
   dvscale = 2, ..., splitter = "Tumor_Sample_Barcode", 
   legcex = 0.8, legy = 7, legxdenom = 3, xaxgen = rainxax, ymax = 8)

Arguments

mut	data frame with mutations on multiple samples, as returned by RTCGAToolbox, for example
colmap	A vector of color names; names of vector elements are nucleotide substitution symbols
oind	index into the set of samples. The function will split the data by sample identifier and sort by number of mutations present (decreasing). oind=1 will select sample with greatest number of mutations; oind=2 will select sample with second greatest, ...
ptcex	cex value for plotting points
dodensity	if TRUE a density estimate will be computed and plotted
inbw	bw setting for stats::density
dvscale	density estimate will be scaled to have maximum value dvscale
...	additional arguments to plot
splitter	name of variable used to split the mutation data.frame into different samples
legcex	cex setting for the legend call
legy	y value for positioning legend
legxdenom	fraction along x axis to at which to center legend
xaxgen	function that generates a call to axis(1, ...)
ymax	ylim setting for plot call

Value

invisibly returns a list with elements mutGR, density, and thecall

Author(s)

VJ Carey <[e-mail]>

References

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3776390&tool=pmcentrez&rendertype=abstract

Examples

data(brcaMuts)
par(mfrow=c(3,1), mar=c(4,6,2,2))
for (i in 1:3) rainfall(brcaMuts, oind=i)

genomicsclass/ph525x documentation built on July 16, 2022, 1:37 p.m.