plotwaterfall: plotwaterfall

Description Usage Arguments Examples

View source: R/visualization.R

Description

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

Usage

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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

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# 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<-"dir"

# 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 Nov. 13, 2020, 5:06 p.m.