maftools (version 0.99.30)

plotCBSsegments: Plots segmented copy number data.

Description

Plots segmented copy number data.

Usage

plotCBSsegments(cbsFile = NULL, maf = NULL, tsb = NULL, chr = NULL,
  savePlot = FALSE, width = 6, height = 3, labelAll = FALSE,
  genes = NULL, writeTable = FALSE)

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 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.

chr

Just plot this chromosome.

savePlot

If true plot is saved as pdf.

width

width of plot

height

height of plot

labelAll

If true and if maf object is specified, maps all mutataions from maf onto segments. Default FALSE, maps only variants on copy number altered regions.

genes

highlight only these variants

writeTable

If true and if maf object is specified, writes plot data with each variant and its corresponding copynumber to an output file.

Value

ggplot object

Details

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

Examples

# NOT RUN {
tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools")
plotCBSsegments(cbsFile = tcga.ab.009.seg)

# }