maftools (version 0.99.30)

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)

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.

Value

a ggplot object which can be further modified.

See Also

oncodrive

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
laml.sig <- oncodrive(maf = laml, AACol = 'Protein_Change', minMut = 5)
plotOncodrive(res = laml.sig, fdrCutOff = 0.1)

# }