Plot Relative Copy Numbers

Just an updated version of the QDNAseq package's plot() method. This version just allows for relative copy number calls from WiseCondorX too. All else remains the same. See the <QDNAseq plotting> method for details.

Usage

RelativeCNSegmentsPlot(
  x,
  main = NULL,
  includeReadCounts = TRUE,
  logTransform = TRUE,
  scale = TRUE,
  sdFUN = "sdDiffTrim",
  delcol = getOption("QDNAseq::delcol", "darkred"),
  losscol = getOption("QDNAseq::losscol", "red"),
  gaincol = getOption("QDNAseq::gaincol", "blue"),
  ampcol = getOption("QDNAseq::ampcol", "darkblue"),
  pointcol = getOption("QDNAseq::pointcol", "black"),
  segcol = getOption("QDNAseq::segcol", "chocolate"),
  misscol = getOption("QDNAseq::misscol", NA),
  pointpch = getOption("QDNAseq::pointpch", 1L),
  pointcex = getOption("QDNAseq::pointcex", 0.1),
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  xaxt = "s",
  yaxp = NULL,
  showDataPoints = TRUE,
  showSD = TRUE,
  doSegments = TRUE,
  doCalls = TRUE,
  ...,
  verbose = getOption("QDNAseq::verbose", TRUE)
)

Details

Supply a QDNAseq object.