plotCR: plots a copy number profile

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

plots a copy number profile

Description

plots a copy number profile

Usage

plotCR(
  cR,
  showClonality = T,
  errorBars = T,
  chr = "all",
  genome = "hg19",
  alpha = 1,
  add = F,
  moveHet = T,
  pt.cex = 1,
  setMargins = T,
  fullFrequency = F,
  colourDeviation = T,
  forceCol = NA,
  plotCall = T,
  plotArrows = F,
  smallPlot = F,
  lwd = 1,
  sep.lwd = 5,
  sideSpace = NULL,
  noSex = F,
  ...
)

Arguments

cR	data.frame. The "clusters" or "CR" from the data.
showClonality	logical. if the clonality panel is shown, if data available. Default TRUE.
errorBars	logical. If errorbars are plotted. Default TRUE.
chr	character. Which chromosome to plot. Default 'all', which plots the entire genome.
genome	character. The genome assembly. Default 'hg19'.
alpha	numeric. The opacity of the point. Default 1.
add	logical. If the data should be plotted on top of whatever is already there. Default FALSE.
moveHet	logical. If the SNP data should snap to f=0.5 if not significantly different. Default TRUE.
pt.cex	numerical. Scaling factor for the size of the points. Default 1.
setMargins	logical. If the margins should be removed to use the entire plottable area. Default TRUE.
fullFrequency	logical. If the SNPs should be copied back up to 1-f as well. Generally not a good idea, and potentially misleading, but can be useful for people that are not used to see frequencies mirrored down to 0-0.5.
colourDeviation	logical. If the points should be coloured based on deviation from diploid. Defaulty TRUE.
forceCol	colour. The colour all the points will be plotted in. Can be useful if overplotting several samples with add=T. Overrides colourDeviation if not NA. Default NA.
plotCall	logical. If the copy number call should be added to the bottom of the SNP panel. Default TRUE.
...	remaining arguments are passed to base plot(...) if add=F, otherwise ignored.

Details

This function plots copy number information from superFreq, either on a by-gene level or by-segment.

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.