plot.coocur: Visualize mutation coocurrence and exclusivity.

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

Description

Visualize mutaiton coocurrence and exclusivity.

Usage

plot.coocur(d, genes=NULL, gene.num=26, dist.to.left=5, discard.syn=F, num.of.smp=NULL, image.color=NULL, show.legend=T, legend.panel=NULL,subtype=NULL,subtype.color=NULL, subtype.labels=NULL,...)

Arguments

d	Mutation matrix with gene and sample names as columan and row names, respectively. The integer in each cell represents different mutation types.
genes	A vector of gene names.
gene.num	The number of top recurrently mutated genes selected for visualization.
dist.to.left	Distance between image to the left hand side margin, increase to if gene symbol truncated.
discard.syn	If TRUE discard syn mutation in calculating gene mutation frequency.
num.of.smp	The number of samples used in calculating gene mutation frequency.
image.color	A vector of 8 elements representing a color scheme.
show.legend	If TRUE draw legend panel
legend.panel	Legend panel, e.g. legend.panel=data.frame(V1=c(7,6,5,4,3,2),V2=c('Nonsense','Splice site','Frame shift','Inframe shift','Missense','Syn.'))
subtype	A vector of subtype, named by samples.
subtype.color	A vector of subtype colors.
subtype.labels	A vector of subtype legend.
...	Parameters pass to image(...).

See Also

mut_cor_permu_test,plot.CoocurExclus

Examples

library(RColorBrewer)
data("CRCMutMat", package='lxctk')
plot.coocur(mutmat, gene.num=26)

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