oncoplot: draw an oncoplot

Description

takes output generated by read.maf and draws an oncoplot (aka waterfall plot).

Usage

oncoplot(maf, writeMatrix = FALSE, top = 20, drawRowBar = TRUE,
  drawColBar = TRUE, showTumorSampleBarcodes = FALSE, annotation = NULL,
  genesToIgnore = NULL, removeNonMutated = FALSE, colors = NULL)

Arguments

maf

an MAF object generated by read.maf

writeMatrix

writes oncomatrix to output file.

top

how many top genes to be drawn. defaults to 20.

drawRowBar

logical plots barplot for each gene.

drawColBar

logical plots barplot for each sample.

showTumorSampleBarcodes

logical to include sample names.

annotation

data.frame with first column containing Tumor_Sample_Barcodes and rest of columns with annotations.

genesToIgnore

do not show these genes in Oncoplot. Default NULL.

removeNonMutated

Logical. If TRUE removes samples with no mutations in the oncoplot for better visualization. Default FALSE.

colors

named vector of colors for each Variant_Classification.

Value

None.

Details

Takes maf file as input and plots it as a matrix. Any desired annotations can be added at the bottom of the oncoplot by providing annotation

Examples

Run this code

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
oncoplot(maf = laml, top = 3)
# }

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