plots a copy number profile
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, ...)data.frame. The "clusters" or "CR" from the data.
logical. if the clonality panel is shown, if data available. Default TRUE.
logical. If errorbars are plotted. Default TRUE.
character. Which chromosome to plot. Default 'all', which plots the entire genome.
character. The genome assembly. Default 'hg19'.
numeric. The opacity of the point. Default 1.
logical. If the data should be plotted on top of whatever is already there. Default FALSE.
logical. If the SNP data should snap to f=0.5 if not significantly different. Default TRUE.
numerical. Scaling factor for the size of the points. Default 1.
logical. If the margins should be removed to use the entire plottable area. Default TRUE.
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.
logical. If the points should be coloured based on deviation from diploid. Defaulty TRUE.
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.
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.
This function plots copy number information from superFreq, either on a by-gene level or by-segment.