R/AbstractCBS.PLOT.R

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

###########################################################################/**
# @set "class=AbstractCBS"
# @RdocMethod plotTracks
#
# @title "Plots the segmentation result along the genome"
#
# \description{
#   @get "title".
# }
#
# @synopsis
#
# \arguments{
#  \item{...}{...}
# }
#
# \value{
#   Returns nothing.
# }
#
# @author "HB"
#
# \seealso{
#   @seeclass
# }
#*/###########################################################################
setMethodS3("plotTracks", "AbstractCBS", abstract=TRUE)


setMethodS3("tileChromosomes", "AbstractCBS", abstract=TRUE, protected=TRUE)


setMethodS3("drawChangePoints", "AbstractCBS", abstract=TRUE, protected=TRUE)


setMethodS3("drawKnownSegments", "AbstractCBS", function(fit, col="#aaaaaa", ..., xScale=1e-6) {
  segs <- fit$params$knownSegments

  # Nothing todo?
  if (is.null(segs)) {
    return()
  }

  # Workaround from the fact that extractChromosomes() does not drop
  # known segments. /HB 2013-03-21
  chromosome <- NULL; rm(list="chromosome") # To please R CMD check.
  segs <- subset(segs, chromosome %in% getChromosomes(fit))
  xStarts <- segs[,"start"]
  xEnds <- segs[,"end"]
  xs <- sort(unique(c(xStarts, xEnds)))
  abline(v=xScale*xs, col=col, ...)
}, protected=TRUE)