maftools (version 0.99.30)

oncostrip: draw an oncostrip similar to cBioportal oncoprinter output.

Description

draw an oncostrip similar to cBioportal oncoprinter output.

Usage

oncostrip(maf, genes = NULL, sort = TRUE, annotation = NULL,
  removeNonMutated = FALSE, top = 5, showTumorSampleBarcodes = FALSE,
  colors = NULL)

Arguments

maf

an MAF object generated by read.maf

genes

draw oncoprint for these genes. default NULL. Plots top 5 genes.

sort

logical sort oncomatrix for enhanced visualization. Defaults to True.

annotation

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

removeNonMutated

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

top

how many top genes to be drawn. defaults to 5.

showTumorSampleBarcodes

logical to include sample names.

colors

named vector of colors for each Variant_Classification.

Value

None.

See Also

oncoplot

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
dev.new()
oncostrip(maf = laml, genes = c('NPM1', 'RUNX1'), removeNonMutated = TRUE)

# }