plotCBSsegments {maftools} | R Documentation

## Plots segmented copy number data.

### Description

Plots segmented copy number data.

### Usage

    plotCBSsegments(
      cbsFile = NULL,
      maf = NULL,
      tsb = NULL,
      savePlot = FALSE,
      ylims = NULL,
      seg_size = 0.1,
      width = 6,
      height = 3,
      genes = NULL,
      ref.build = "hg19",
      writeTable = FALSE,
      removeXY = FALSE,
      color = NULL
    )

### Arguments

`cbsFile` | CBS segmented copy number file. Column names should be Sample, Chromosome, Start, End, Num_Probes and Segment_Mean (log2 scale).
`maf` | optional `MAF`
`tsb` | If segmentation file contains many samples (as in gistic input), specify sample name here. Defualt plots head 1 sample. Set 'ALL' for plotting all samples. If you are maping maf, make sure sample names in Sample column of segmentation file matches to those Tumor_Sample_Barcodes in MAF.
`savePlot` | If true plot is saved as pdf.
`ylims` | Default NULL
`seg_size` | Default 0.1
`width` | width of plot
`height` | height of plot
`genes` | If given and maf object is specified, maps all mutataions from maf onto segments. Default NULL
`ref.build` | Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.
`writeTable` | If true and if maf object is specified, writes plot data with each variant and its corresponding copynumber to an output file.
`removeXY` | don not plot sex chromosomes.
`color` | Manually specify color scheme for chromosomes. Default NULL. i.e, aletrnating Gray70 and midnightblue

### Details

this function takes segmented copy number data and plots it. If MAF object is specified, all mutations are highlighted on the plot.

### Value

Draws plot

### Examples

    tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools")
    plotCBSsegments(cbsFile = tcga.ab.009.seg)

[Package maftools version 2.10.05 Index]