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

Description Usage Arguments Details See Also Examples

View source: R/plot.spectra.R

Description

plot mutation spectrum.

Usage

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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

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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.