R/plotObs.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

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## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
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### Function that plots a vector of copy numbers

### INPUT:
### type: what kind of plot is this? may be "sample","chromosome","genome" or "aspcf"
### y   : a vector of data points to be plotted;
### pos : a vector of positions to be plotted along x-axis
### unit: the unit used to represent probe positions (bp / kbp / mbp)
### winsoutliers: a vector giving winsorization outlier statuses for data points in y
### xaxis: a string indicating whether positions ("pos") or indeces ("index") should be plotted on xaxis
### plot.ideo: will ideogram be plotted?
### k: the chromosome number being plotted; only applicable for type="sample" or if print.xwarn..
### sampleID: the id of the sample being plotted; only applicable for type="chromosome" and type="genome"
### chromosomes: a vector of same length as pos giving the corrosponding chromosome numbers (only used when type="genome")
### frame: the frame dimensions for this plot
### new: has a new plot already been started?
### print.xwarn: should a warning be printed if the input positions exceed the chromosome range in cytoband?  st the moment always FALSE
### seg.lim:  ylimits for segments ; check whether this should be adjusted for q
### data.lim: ylimits for data points (adjusted for q and equalRange)
### op:  other parameters
### xmax: maximum on x-axis, will be NULL if ideogram is not plotted


## Required by:
### plotAllele
### plotChrom
### plotGenome
### plotSample


## Requires:
### addChromlines
### addToPlot
### getPlotSymbols
### getx
### updatePlotParameters

plotObs <- function(type, y, pos, unit, winsoutliers, xaxis, plot.ideo = FALSE, k = NULL, sampleID = NULL, frame = NULL, new = FALSE, print.xwarn = FALSE, seg.lim = NULL, op, xmax = NULL, chromosomes = NULL, data.lim = NULL) {
  # Pick out what should be plotted on x-axis (position or index). If type=genome positions are converted to global positions
  x <- getx(xaxis, type, chromosomes, pos, unit, op)
  if (is.null(xmax)) {
    xmax <- max(x)
  }

  # Update diverse plotparameters (ylim,xlim,main,ticks,mar)
  op <- updatePlotParameters(seg.lim = seg.lim, xmax = xmax, type = type, xaxis = xaxis, op = op, data.lim = data.lim, sampleID = sampleID, k = k)

  # Get colours, symbols and size for plotting observations. Truncate observations outside limits
  s <- getPlotSymbols(y, winsoutliers, type, x, xmax, print.xwarn, k, op)
  colobs <- s$colobs
  pch.obs <- s$pch.obs
  cex.obs <- s$cex.obs
  # The values for border-observations have been truncated
  x <- s$x
  y <- s$y

  # PLOT OBSERVED DATA:

  # Empty plot with right dimensions:
  par(fig = unlist(frame), new = new, mar = op$mar)
  plot(x, y, ylab = "", xlab = "", main = "", pch = pch.obs, cex = cex.obs, col = colobs, ylim = op$ylim, xlim = op$xlim, xaxt = "n", yaxt = "n", xaxs = "i", yaxs = "r")

  # Add axes, labels, title and reference line
  addToPlot(plot.ideo, op, type = type)

  # Separate chromosomes by vertical lines (only done for type=="genome")
  if (type == "genome") {
    addChromlines(chromosomes, xaxis, unit, cex = op$cex.chrom, op = op)
  }
} # endplotObs