maftools: plotOncodrive – R documentation

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plotOncodrive

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,
  bubbleSize = 1,
  labelSize = 1
)

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
`bubbleSize`	Size for bubbles. Default 2.
`labelSize`	font size for labelling genes. Default 1.

Value

Nothing

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)

maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05

MIT + file LICENSE

Authors

Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)

Initial release

2015-12-14