oncostrip {maftools}R Documentation

draw an oncostrip similar to cBioportal oncoprinter output.

Description

draw an oncostrip similar to cBioportal oncoprinter output.

Usage

oncostrip(maf, genes = NULL, top = 5, colors = NULL, sort = TRUE,
  clinicalFeatures = NULL, annotationDat = NULL,
  sortByAnnotation = FALSE, annotationOrder = NULL,
  removeNonMutated = TRUE, showTumorSampleBarcodes = FALSE,
  annotationColor = NULL, fontSize = 10, titleFontSize = 15,
  legendFontSize = 12, bgCol = "#CCCCCC", borderCol = NA)

Arguments

maf

an MAF object generated by read.maf

genes

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

top

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

colors

named vector of colors for each Variant_Classification.

sort

logical sort oncomatrix for enhanced visualization. Defaults to TRUE.

clinicalFeatures

columns names from 'clinical.data' slot of MAF to be drawn in the plot. Dafault NULL.

annotationDat

If MAF file was read without annotations, provide a custom data.frame with a column containing Tumor_Sample_Barcodes along with rest of columns with annotations. You can specify which columns to be drawn using 'clinicalFeatures' argument.

sortByAnnotation

logical sort oncomatrix (samples) by provided 'clinicalFeatures' Defaults to FALSE. column-sort.

annotationOrder

Manually specify order for annotations. Works only for first 'clinicalFeatures'. Default NULL.

removeNonMutated

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

showTumorSampleBarcodes

logical to include sample names.

annotationColor

list of colors to use for 'clinicalFeatures'. Must be a named list. Default NULL.

fontSize

font size for gene names. Default 10.

titleFontSize

font size for title. Default 15

legendFontSize

font size for legend. Default 12

bgCol

Background grid color for wild-type (not-mutated) samples. Default gray - "#CCCCCC"

borderCol

border grid color for wild-type (not-mutated) samples. Default NA.

Value

None.

See Also

oncoplot

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
dev.new()
oncostrip(maf = laml, genes = c('NPM1', 'RUNX1'))


[Package maftools version 1.8.0 Index]