Plot oncogenic pathways
Plot oncogenic pathways
PlotOncogenicPathways( maf, pathways = NULL, fullPathway = FALSE, removeNonMutated = TRUE, tsgCol = "red", ogCol = "royalblue", fontSize = 0.6, showTumorSampleBarcodes = FALSE, sampleOrder = NULL, SampleNamefontSize = 0.6 )
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 |
Draws oncoplot of oncogenic pathway.
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
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
PlotOncogenicPathways(maf = laml, pathways = "RTK-RAS")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.