plot.96.spectra: Visualize mutation spectra in 96 contexts

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

plot mutation spectra at 96 alphabetically sorted contexts.

Usage

plot.96.spectra(x, col=brewer.pal(6, "Paired"), main="spectra.96", max.ylim=NA, draw.legend=TRUE, bottom=FALSE)

Arguments

x	The (relative) frequency of mutations at 96 alphabetically sorted contexts.
col	A vector of colors used.
main	The main title.
max.ylim	max ylim.
draw.legend	If TRUE, add legend to current panel.
bottom	Should legend be placed at the bottom?.

Examples

library(RColorBrewer)
data("spectra.96")
x <- spectra.96['67-VS-67TB',]
plot.96.spectra(x)

Multipe plots in a panel, e.g.

pdf("spectra.pdf", width=9, height=7)
par(mfrow=c(6,2), family="sans")
plot.96.spectra(spectra.96['67-VS-67TB',], main="29-VS-29TB")
plot.96.spectra(spectra.96['29-VS-29TB',], main="29-VS-29TB")
plot.96.spectra(spectra.96['3-VS-3TB',], main="3-VS-3TB")
plot.96.spectra(spectra.96['32-VS-29TB',], main="32-VS-29TB")
plot.96.spectra(spectra.96['87-VS-87-TB',], main="87-VS-87-TB")
plot.96.spectra(spectra.96['86-VS-87-TB',], main="86-VS-87-TB")
plot.96.spectra(spectra.96['69-VS-3TB',], main="69-VS-3TB")
plot.96.spectra(spectra.96['88-VS-67TB',], main="88-VS-67TB")
plot.96.spectra(spectra.96['sample_7-3-VS-sample_7-1',], main="sample_7-3-VS-sample_7-1")
plot.96.spectra(spectra.96['sample_7-2-VS-sample_7-1',], main="sample_7-2-VS-sample_7-1")
plot.96.spectra(spectra.96['sample_8-3-VS-sample_8-1',], main="sample_8-3-VS-sample_8-1")
plot.96.spectra(spectra.96['sample_8-2-VS-sample_8-1',], main="sample_8-2-VS-sample_8-1")
dev.off()

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.