plotOncodrive {maftools} | R Documentation

## Plots results from `oncodrive`

### Description

Takes results from `oncodrive` and plots them as a scatter plot. Size of the gene shows number of clusters (hotspots), x-axis can either be an absolute number of variants accumulated in these clusters or a fraction of total variants found in these clusters. y-axis is fdr values transformed into -log10 for better representation. Labels indicate Gene name with number clusters observed.

### Usage

    plotOncodrive(res = NULL, fdrCutOff = 0.05, useFraction = FALSE,
      colCode = NULL, labelSize = 2)

### Arguments

`res` | results from `oncodrive`
`fdrCutOff` | fdr cutoff to call a gene as a driver.
`useFraction` | if TRUE uses a fraction of total variants as X-axis scale instead of absolute counts.
`colCode` | Colors to use for indicating significant and non-signififcant genes. Default NULL
`labelSize` | font size for labelling genes. Default 2.

### Value

a ggplot object which can be further modified.

### See Also

`oncodrive`

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    laml.sig <- oncodrive(maf = laml, AACol = 'Protein_Change', minMut = 5)
    plotOncodrive(res = laml.sig, fdrCutOff = 0.1)

[Package maftools version 1.8.0 Index]