ggPlotMutationalSignatures: Plotting mutational signatures

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

Description

Plotting mutational signatures.

Usage

ggPlotMutationalSignatures(mutational.processes.file, d=NULL, color_pallete="Dark2", xlabel="Mutational contexts", ylabel="Percentage of mutations", y.upper.value=NA)

Arguments

mutational.processes.file	Mutational process file obtained after running decipherMutationalSignatures. See github https://github.com/lixiangchun/decipherMutationalSignatures for more information.
d	A data frame refers to mutational.processes.file.
color_pallete	The name of color pallete supported by ColorBrewer.
xlabel	X-label.
ylabel	Y-label.
y.upper.value	Truncate y-value to this value if provided (range: 0-100).

Value

A ggplot object.

See Also

SomaticSignatures::plotSignatures

Examples

infile='/Users/lixiangchun/Public/WorkSpace/Project/TJMUCH-Prof.ChenKexin-CRC/lixc/revision/decipherMutationalSignatures/output/Rank_eq_3.processes.txt'
ggPlotMutationalSignatures(infile)

# Or

d=read.table(infile,header=TRUE,stringsAsFactors=FALSE)
x=d[,c(1,2,4,5,3)]
colnames(x)[3:5] = c('Signature1','Signature2', 'Signature3')
ggPlotMutationalSignatures(d=x)

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