plot.mutational.exposures: Visualizing mutational exposures.

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

Description

Visualizing mutational exposures.

Usage

plot.mutational.exposures(d = NULL,
           mutational.exposure.file = NULL,
           clustid = NULL,
           cols =  c('#6C4F4C','#8EA37A','#843818','#AEDD99','#F89867','#FF0000','#A79D90'),
           sorting = FALSE,
           use.colname.as.signature.name = FALSE,
           legend.ncol = 4,
           legend.ypos = 0,
           sorting.by.sample.name = FALSE,
           add.sample.name = FALSE)

Arguments

d	A data frame of mutational exposures. Check example for more info about the file format.
mutational.exposure.file	Mutational exposure file outputted from mutational signature deciphering framework https://github.com/lixiangchun/decipherMutationalSignatures.
clustid	A vector of clustid of each sample.
cols	A vector of colors used.
sorting	If TRUE, sort exposures sequentially.
legend.ypos	The y-position of the legend.

Details

See the following example for more info about inputs.

See Also

plot.mutational.processes

Examples

library(lxctk)
data("icgc.hcc", package="lxctk") ## ICGC liver cancer data and SMGs selected for NMF clustering.

d <- icgc.hcc
mutationalSignatureNames <- paste('mutationalSignature',1:7,sep="")
clustid <- d$nmf_clustid
# clustid <- rep(0, nrow(d))

plot.mutational.exposures(d[,mutationalSignatureNames])

# Or
plot.mutational.exposures(d[,mutationalSignatureNames],clustid)

## Or
plot.mutational.exposures(NULL,system.file('data/Rank_eq_9.exposures.txt',package='lxctk'))

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