plotPathways: Plot oncogenic pathways

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Plot oncogenic pathways

Description

Plot oncogenic pathways

Usage

plotPathways(
  maf = NULL,
  pathlist = NULL,
  pathnames = NULL,
  removeNonMutated = FALSE,
  fontSize = 1,
  showTumorSampleBarcodes = FALSE,
  sampleOrder = NULL,
  SampleNamefontSize = 0.6,
  mar = c(4, 6, 2, 3)
)

Arguments

maf	an MAF object
pathlist	Output from pathways
pathnames	Names of the pathways to be drawn. Default NULL, plots everything from input 'pathlist'
removeNonMutated	Default FALSE
fontSize	Default 1
showTumorSampleBarcodes	logical to include sample names.
sampleOrder	Manually speify sample names for oncolplot ordering. Default NULL.
SampleNamefontSize	font size for sample names. Default 0.6
mar	margins Default c(4, 6, 2, 3). Margins to bottom, left, top and right respectively

Details

Draws pathway burden123

References

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S et al. 2018. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173: 321-337 e310

See Also

pathways

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
p <- pathways(maf = laml)
plotPathways(maf = laml, pathlist = p)

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.