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 1.6.15 Index]