plot.spectra: Visualize mutation spectra in 6 or 8 contexts

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

Description

plot mutation spectrum.

Usage

plot.spectra(d, frequency=TRUE, col=brewer.pal(dim(d)[2], "Dark2"), cex.tck=0.7, show.smp.name=TRUE, pdffig=NA, ...)

Arguments

d	A matrix with sample as row name and mutation category as columan name.
frequency	Plot the number of mutation instead of fraction.
col	Color scheme for mutation spectrum.
cex.tck	cex for tick label.
show.smp.name	if FALSE, does not show sample name.
pdffig	file name of figure to be saved.
...	Additional parameters passed to barplot, e.g. main, ylab.

Details

Set border=NA to omit bar border entirely.

See Also

plot.96.spectra, plot.depth

Examples

library(RColorBrewer)
library(lxctk)
data("muSpec")
plot.spectra(muSpec8, frequency=TRUE, ylab="Number of mutations", main="Mutation Spectra")
plot.spectra(muSpec8, frequency=FALSE, ylab="Mutation type fraction(%)", main="Mutation Spectra")

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