plot.coocur2: Visualize mutation coocurrence and exclusivity.

Description Usage Arguments See Also Examples

View source: R/plot.coocur2.R

Description

Visualize mutaiton coocurrence and exclusivity.

Usage

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plot.coocur2(d, genes=NULL, sort.by.freq=TRUE, k=2, gene.num=26, right.panel=NULL, right.panel.col=NULL, 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,subtype.legend=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.

sort.by.freq

If genes is not NULL, sort by mutation frequency.

k

Mutation type >k is considered nonsilent, otherwise it is silent. Only applicable when sort.by.freq=TRUE.

gene.num

The number of top recurrently mutated genes selected for visualization.

right.panel

right panel data.

right.panel.col

right panel color.

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.

subtype.legend

A data.frame of subtype legend.

...

Parameters pass to image(...).

See Also

mut_cor_permu_test,plot.CoocurExclus,plot.coocur

Examples

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data('plot.coocur2.test')
plot.coocur2(dat,MutationForValidate$Wnt_pathway, right.panel=right.panel, right.panel.col=right.panel.col, subtype=subtype, subtype.color=brewer.pal(9, "Paired"), subtype.labels=c("Location ", "Stage ", "Lauren's type"), subtype.legend=legend.panel.df)

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