plot.mutational.processes: Plot mutational processes obtaining from mutational signature...

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

Description

Plot mutational processes obtaining from mutational signature deciphering framework (https://github.com/lixiangchun/decipherMutationalSignatures).

Usage

plot.mutational.processes(d=NULL, mutational.processes.file = NULL,
  color=brewer.pal(6, "Paired"), main='Mutational Signature', 
  sig.labs=NULL, figpdf='mutation_signature.pdf')

Arguments

d	Mutational signatures in data.frame. Check example for data format. Note that the first and second column names must be subtypes and types, respectively.
mutational.processes.file	Mutational process file obtained after running decipherMutationalSignatures. See github https://github.com/lixiangchun/decipherMutationalSignatures for more information.
color	Colors for each mutational signature.
main	Title for mutational signature plot.
sig.labs	Labels of mutational signatures.
figpdf	Output fig if provided.

See Also

sort.data.frame

Examples

data('plot.mutation.signature.ex')
plot.mutation.signature(df, figpdf=NULL)

# Or
plot.mutation.signature(df)

## Not run
plot.mutational.processes(mutational.processes.file = system.file('data/Rank_eq_9.processes.txt',package='lxctk'), figpdf=NULL)

plot.mutational.processes(mutational.processes.file = system.file('data/Rank_eq_5.processes.txt',package='lxctk'))

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