plotCNA: plotCNA

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

plotCNA

Usage

plotCNA(
  seg,
  patient.id = NULL,
  sampleOrder = NULL,
  chrSilent = NULL,
  refBuild = "hg19",
  sample.text.size = 11,
  chrom.text.size = 3,
  legend.text.size = 9,
  legend.title.size = 11,
  annot.text.size = 3,
  sample.bar.height = 0.5,
  chrom.bar.height = 0.5,
  showRownames = TRUE,
  removeEmptyChr = TRUE,
  showCytoband = FALSE,
  showGene = FALSE,
  use.tumorSampleLabel = FALSE
)

Arguments

seg	Object generated by readSegment function.
patient.id	Select the specific patients. Default NULL, all patients are included.
sampleOrder	A named list which contains the sample order used in plotting the final profile. Default NULL.
chrSilent	Chromosomes excluded in the analysis. e.g, 1, 2, 3. Default NULL.
refBuild	Human reference genome versions of hg18, hg19 or hg38 by UCSC. Default "hg19".
sample.text.size	Fontsize of sample name. Default 11.
chrom.text.size	Fontsize of chromosome text. Default 3.
legend.text.size	Fontsize of legend text. Default 9.
legend.title.size	Fontsize of legend title. Default 11.
annot.text.size	Fontsize of cytoband or gene symbols. Default 3.
sample.bar.height	Bar height of each sample. Default 0.5.
chrom.bar.height	Bar height of each chromosome. Default 0.5.
showRownames	Logical (Default: TRUE). Show sample names of rows.
removeEmptyChr	Remove empty chromosomes that do not exist in all samples. Default TRUE.
showCytoband	Logical (Default: FALSE). Show cytobands on the plot. Only when the seg object is created with GISTIC results, this parameter can be TRUE.
showGene	Logical (Default: FALSE). Show gene symbols on the plot. Only when the seg object is created with txdb, this parameter can be TRUE.
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'.

Value

a heatmap plot of CNA profile

Examples

segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit")
seg <- readSegment(segFile = segFile)
plotCNA(seg)

## showCytoband
gisticAmpGenesFile <- system.file("extdata", "COREAD_amp_genes.conf_99.txt", package = "MesKit")
gisticDelGenesFile <- system.file("extdata", "COREAD_del_genes.conf_99.txt", package = "MesKit")
gisticAllLesionsFile <- system.file("extdata", "COREAD_all_lesions.conf_99.txt", package = "MesKit")
seg <- readSegment(segFile = segFile,
                   gisticAmpGenesFile = gisticAmpGenesFile,
                    gisticDelGenesFile = gisticDelGenesFile,
                   gisticAllLesionsFile = gisticAllLesionsFile)
plotCNA(seg, showCytoband = TRUE)

MesKit documentation built on March 28, 2021, 6 p.m.