plotCoocMutex: plotCoocMutex

In SMDIC: Identification of Somatic Mutation-Driven Immune Cells

plotCoocMutex

Description

Function 'plotCoocMutex' plots the co-occurrence and mutual exclusivity plots for mutation genes which drive immune cells.

Usage

plotCoocMutex(maffile, mutcell.summary, cellnumcuoff = 3, fontSize = 0.8)

Arguments

maffile	The name of mutation annotation file (MAF) format data. It must be an absolute path or the name relatived to the current working directory.
mutcell.summary	The result of 'mutcellsummary' function
cellnumcuoff	A threshold value (4 as the default value). The mutation genes which drive at least "cellnumcuoff" cells are retained for drawing a co-occurrence and mutual exclusivity plots.
fontSize	cex for gene names. Default 0.8

References

Gerstung M, Pellagatti A, Malcovati L, et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nature Communications. 2015;6:5901. doi:10.1038/ncomms6901.

Examples

# get the result of `exp2cell` funtion
cellmatrix<-GetExampleData("cellmatrix")

#get the binary mutations matrix,
mutmatrix<-GetExampleData("mutmatrix")

# get the result of `mutcorcell` funtion
mutcell<-GetExampleData("mutcell")

#perform the function mutcellsummary
summary<-mutcellsummary(mutcell = mutcell,mutmatrix = mutmatrix,cellmatrix=cellmatrix)

#dir is the name of mutation annotation file (MAF) format data.
#It must be an absolute path or the name relatived to the current working directory.
maf<-system.file("extdata", "example.maf.gz", package = "SMDIC") #MAF file
#plot the co-occurrence and mutual exclusivity plots for mutation genes which drive immune cells.
plotCoocMutex(maffile = maf,mutcell.summary = summary,cellnumcuoff =0)

SMDIC documentation built on Oct. 18, 2024, 9:07 a.m.