plotwaterfall: plotwaterfall

In SMDIC: Identification of Somatic Mutation-Driven Immune Cells

plotwaterfall

Description

Function 'plotwaterfall' plots the waterfall for mutation genes which drive immune cells.

Usage

plotwaterfall(
  maffile,
  mutcell.summary,
  cellnumcuoff = 3,
  fontSize = 0.8,
  showTumorSampleBarcodes = F,
  showTitle = TRUE,
  colors = NULL
)

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 (3 as the default value). The mutation genes which drive at least "cellnumcuoff" cells are retained for drawing an waterfall.
fontSize	font size for gene names. Default 0.8.
showTumorSampleBarcodes	logical to include sample names.
showTitle	Default TRUE
colors	named vector of colors for each Variant_Classification.

Examples

# get 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
# mutcell.summary is the result of function mutcellsummary

#plot the waterfall for mutation genes which drive immune cells
plotwaterfall(maffile = maf,mutcell.summary = summary,cellnumcuoff =3)

SMDIC documentation built on Aug. 29, 2023, 5:11 p.m.