Plots segmented copy number data.
Plots segmented copy number data.
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 )
cbsFile |
CBS segmented copy number file. Column names should be Sample, Chromosome, Start, End, Num_Probes and Segment_Mean (log2 scale). |
maf |
optional |
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 |
this function takes segmented copy number data and plots it. If MAF object is specified, all mutations are highlighted on the plot.
Draws plot
tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools")
plotCBSsegments(cbsFile = tcga.ab.009.seg)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.