PlotOncogenicPathways: Plot oncogenic pathways

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Plot oncogenic pathways

Usage

PlotOncogenicPathways(
  maf,
  pathways = NULL,
  fullPathway = FALSE,
  removeNonMutated = TRUE,
  tsgCol = "red",
  ogCol = "royalblue",
  fontSize = 0.6,
  showTumorSampleBarcodes = FALSE,
  sampleOrder = NULL,
  SampleNamefontSize = 0.6
)

Arguments

maf	an MAF object generated by read.maf
pathways	Name of pathways to be drawn
fullPathway	Include all genes from the pathway. Defaulr FALS only plots mutated genes
removeNonMutated	Default TRUE
tsgCol	Color for tumro suppressor genes. Default red
ogCol	Color for onco genes. Default royalblue
fontSize	Default 0.6
showTumorSampleBarcodes	logical to include sample names.
sampleOrder	Manually speify sample names for oncolplot ordering. Default NULL.
SampleNamefontSize	font size for sample names. Default 10

Details

Draws oncoplot of oncogenic pathway.

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

OncogenicPathways

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
PlotOncogenicPathways(maf = laml, pathways = "RTK-RAS")

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.396s elapsed (0.362s cpu) 

maftools documentation built on Feb. 6, 2021, 2 a.m.