plot.coocur2: Visualize mutation coocurrence and exclusivity.
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments See Also Examples

Visualize mutaiton coocurrence and exclusivity.

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,...)

`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(...).

mut_cor_permu_test,plot.CoocurExclus,plot.coocur

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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)