rainfall | R Documentation |
produce an embellished rainfall plot using TCGA mutation data
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)
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 |
invisibly returns a list with elements mutGR, density, and thecall
VJ Carey <stvjc@channing.harvard.edu>
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3776390&tool=pmcentrez&rendertype=abstract
data(brcaMuts) par(mfrow=c(3,1), mar=c(4,6,2,2)) for (i in 1:3) rainfall(brcaMuts, oind=i)
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