oncoplot {maftools}R Documentation

draw an oncoplot

Description

takes output generated by read.maf and draws an oncoplot

Usage

oncoplot(maf, top = 20, genes = NULL, mutsig = NULL,
  mutsigQval = 0.1, drawRowBar = TRUE, drawColBar = TRUE,
  clinicalFeatures = NULL, annotationDat = NULL,
  annotationColor = NULL, genesToIgnore = NULL,
  showTumorSampleBarcodes = FALSE, removeNonMutated = TRUE,
  colors = NULL, sortByMutation = FALSE, sortByAnnotation = FALSE,
  annotationOrder = NULL, keepGeneOrder = FALSE,
  GeneOrderSort = TRUE, sampleOrder = NULL, writeMatrix = FALSE,
  fontSize = 10, SampleNamefontSize = 10, titleFontSize = 15,
  legendFontSize = 12, annotationFontSize = 12,
  annotationTitleFontSize = 12, bgCol = "#CCCCCC", borderCol = NA,
  colbar_pathway = FALSE)

Arguments

maf

an MAF object generated by read.maf

top

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

genes

Just draw oncoplot for these genes. Default NULL.

mutsig

Mutsig resuts if availbale. Usually file named sig_genes.txt If provided plots significant genes and correpsonding Q-values as side row-bar. Default NULL.

mutsigQval

Q-value to choose significant genes from mutsig results. Default 0.1

drawRowBar

logical plots barplot for each gene. Default TRUE.

drawColBar

logical plots barplot for each sample. Default 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 clinical data, 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.

annotationColor

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

genesToIgnore

do not show these genes in Oncoplot. Default NULL.

showTumorSampleBarcodes

logical to include sample names.

removeNonMutated

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

colors

named vector of colors for each Variant_Classification.

sortByMutation

Force sort matrix according mutations. Helpful in case of MAF was read along with copy number data. Default FALSE.

sortByAnnotation

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

annotationOrder

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

keepGeneOrder

logical whether to keep order of given genes. Default FALSE, order according to mutation frequency

GeneOrderSort

logical this is applicable when 'keepGeneOrder' is TRUE. Default TRUE

sampleOrder

Manually speify sample names for oncolplot ordering. Default NULL.

writeMatrix

writes character coded matrix used to generate the plot to an output file. This can be used as an input for ComplexHeatmap oncoPrint function if you wish to customize the plot.

fontSize

font size for gene names. Default 10.

SampleNamefontSize

font size for sample names. Default 10

titleFontSize

font size for title. Default 15

legendFontSize

font size for legend. Default 12

annotationFontSize

font size for annotations. Default 12

annotationTitleFontSize

font size for annotation title. 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.

colbar_pathway

Draw top column bar with respect to diplayed pathway. Default FALSE

Details

Takes maf file as input and plots it as a matrix. Any desired clincal features can be added at the bottom of the oncoplot by providing clinicalFeatures. Oncoplot can be sorted either by mutations or by clinicalFeatures using arguments sortByMutation and sortByAnnotation respectively.

Value

None.

See Also

oncostrip

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
oncoplot(maf = laml, top = 3)

[Package maftools version 1.8.0 Index]