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,
  includeColBarCN = TRUE, draw_titv = FALSE, logColBar = FALSE,
  clinicalFeatures = NULL, exprsTbl = NULL, additionalFeature = NULL,
  additionalFeaturePch = 20, additionalFeatureCol = "white",
  additionalFeatureCex = 0.9, annotationDat = NULL,
  annotationColor = NULL, genesToIgnore = NULL,
  showTumorSampleBarcodes = FALSE, removeNonMutated = TRUE,
  fill = FALSE, colors = NULL, sortByMutation = FALSE,
  sortByAnnotation = FALSE, numericAnnoCol = NULL,
  groupAnnotationBySize = TRUE, annotationOrder = NULL,
  keepGeneOrder = FALSE, GeneOrderSort = TRUE, sampleOrder = NULL,
  writeMatrix = FALSE, fontSize = 0.8, SampleNamefontSize = 1,
  titleFontSize = 1.5, legendFontSize = 1.2,
  annotationFontSize = 1.2, bgCol = "#CCCCCC", borderCol = "white",
  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.

includeColBarCN

Whether to include CN in column bar plot. Default TRUE

draw_titv

logical Includes TiTv plot. FALSE

logColBar

Plot top bar plot on log10 scale. Default FALSE.

clinicalFeatures

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

exprsTbl

Expression values if availble. Must be a data.frame with two columns containing to gene names and expression values.

additionalFeature

a vector of length two indicating column name in the MAF and the factor level to be highlighted.

additionalFeaturePch

Default 20

additionalFeatureCol

Default "white"

additionalFeatureCex

Default 0.9

annotationDat

If MAF file was read without clinical data, provide a custom data.frame with a column Tumor_Sample_Barcode containing sample names 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.

fill

Logical. If TRUE draws genes and samples as blank grids even when they are not altered.

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

numericAnnoCol

color palette used for numeric annotations. Default 'YlOrBr' from RColorBrewer

groupAnnotationBySize

Further group 'sortByAnnotation' orders by their size. Defaults to TRUE. Largest groups comes first.

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.

fontSize

font size for gene names. Default 0.8.

SampleNamefontSize

font size for sample names. Default 1

titleFontSize

font size for title. Default 1.5

legendFontSize

font size for legend. Default 1.2

annotationFontSize

font size for annotations. Default 1.2

bgCol

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

borderCol

border grid color (not-mutated) samples. Default 'white'.

colbar_pathway

Draw top column bar with respect to diplayed pathway. Default FALSE. Not implemented yet!

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 2.0.0 Index]