PlotOncogenicPathways {maftools} | R Documentation

## Plot oncogenic pathways

### 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")

[Package maftools version 2.4.12 Index]