plotCopyNumbers: plot Copy Numbers from ASCAT-like file

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

plot Copy Numbers from ASCAT-like file

Description

Plot the copy numbers across the Chromosomes. Optionally, plot also highlight regions at the bottom. For example, could be used to highlight HRD-LOH regions.

Usage

plotCopyNumbers(
  sv_df,
  sample_name,
  filename = NULL,
  plottitle = NULL,
  mar = NULL,
  minorCNcolour = "green",
  totalCNcolour = "red",
  outofrangeCNcolour = "purple",
  highlightRegions = NULL,
  highlightText = NULL,
  highlightColour = "brown",
  textscaling = 1,
  genome.v = "hg19"
)

Arguments

sv_df	data frame with the following columns: 'seg_no', 'Chromosome', 'chromStart', 'chromEnd', 'total.copy.number.inNormal', 'minor.copy.number.inNormal', 'total.copy.number.inTumour', 'minor.copy.number.inTumour'
sample_name	sample name
filename	if a file name is specified, a pdf file will be generated
mar	set custom margins, otherwise mar will be set to mar = c(4,4,3,2)
highlightRegions	dataframe with columns 'Chromosome', 'Start', 'End', which specify the regions to highlight. This is optional.
highlightText	if highlightRegions is specified, then highlightText will be plotted in the bottom right
highlightColour	set the colour of the highlight regions and text. Default is brown

Value

returns the HRD-LOH index or regions

Examples

ascat.data <- read.table("ascat.scv",sep=",",header=TRUE)
HRDLOHregions <- ascatToHRDLOH(ascat.df,"test_sample",return.loc=TRUE)
HRDLOHscore <- nrow(HRDLOHregions)
plotCopyNumbers(sv_df = ascat.data,sample_name = "",highlightRegions = HRDLOHregions,
                highlightText = paste0("HRD-LOH\\n",HRDLOHscore))

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.