jointseg (version 1.0.2)

plotSeg: Plot signal and breakpoints with segment-level signal estimates

Description

Plot signal and breakpoints with segment-level signal estimates

Usage

plotSeg(dat, breakpoints = NULL, regNames = NULL,
  exclNames = c("genotype", "region", "bT", "bN", "cellularity"),
  ylabs = colnames(dat), ylims = NULL, binExclPattern = "^b[N|T]*$",
  col = "#33333333", pch = 19, cex = 0.3)

Arguments

dat

A matrix or data frame whose rows correspond to loci sorted along the genome, or a numeric vector.

breakpoints

A vector of breakpoints positions, or a list of such vectors.

regNames

Region labels, a vector of length length(breakpoints)+1 (if breakpoints is a vector) or of length length(breakpoints[[1]])+1 (if breakpoints is a list).

exclNames

A vector of column names corresponding to columns that should not be plotted.

ylabs

A vector of 'y' labels (column names or indices) that should be plotted.

ylims

An optional \(2*d\) matrix with ylim values for each of the \(d\) dimensions to be plotted.

binExclPattern

A vector of column names or indices in colnames(dat) for which segment-level signal estimates should *not* be drawn.

col

Color of plotting symbol, see par

pch

Plotting symbol, see par

cex

Magnification factor for plotting symbol, see par

Details

Argument 'binCols' is mainly used to avoid calculating mean levels for allelic ratios, which would not make sense as they are typically multimodal.

Examples

# NOT RUN {
affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
sim <- getCopyNumberDataByResampling(1e4, 5, minLength=100, regData=affyDat)
dat <- sim$profile
res <- PSSeg(dat, method="RBS", stat=c("c", "d"), K=50)
bkpList <- list(true=sim$bkp, est=res$bestSeg)
plotSeg(dat, breakpoints=bkpList)
# }