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 1.6.15 Index]