R/AllelicCrosstalkCalibration.PLOT.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("plotAllelePairs", "AllelicCrosstalkCalibration", function(this, array, pairs=NULL, what=c("input", "output"), ..., pch=".", cex=1, lty=3, xlim=c(-500,2^16), ylim=xlim, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'array':
  array <- Arguments$getIndex(array, range=c(1, Inf))

  # Argument 'pairs':
  if (is.null(pairs)) {
  } else {
    pairs <- Arguments$getIndices(pairs, max=999)
  }

  # Argument 'what':
  what <- match.arg(what)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Get data set of interest
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (what == "input") {
    ds <- getInputDataSet(this)
  } else if (what == "output") {
    if (!isDone(this)) {
      throw("Cannot plot allele-pair signals for output data set. Data is still not calibrated.")
    }
    ds <- getOutputDataSet(this)
  }

  # Get the array of interest
  df <- ds[[array]]


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Get the sets of cell-index pairs of interest
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  setsOfProbes <- getSetsOfProbes(this, verbose=less(verbose, 5))
  setsOfProbes <- setsOfProbes$snps
  nbrOfPairs <- length(setsOfProbes)
  if (is.null(pairs)) {
    pairs <- seq_len(nbrOfPairs)
  } else {
    pairs <- Arguments$getIndices(pairs, max=nbrOfPairs)
    nbrOfPairs <- length(pairs)
  }

  # Sanity check
  if (nbrOfPairs < 1) {
    throw("No allele pairs to plot")
  }

  # Extract cell pairs of interest
  setsOfProbes <- setsOfProbes[pairs]


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Plot data
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Set up the plot grid
  layout(matrix(seq_len(nbrOfPairs), nrow=floor(sqrt(nbrOfPairs))))
  par(mar=c(3,3,1,1)+0.1, mgp=c(1.8,0.5,0), oma=c(0,0,3,0))
  for (kk in seq_len(nbrOfPairs)) {
    cells <- setsOfProbes[[kk]]
    name <- names(setsOfProbes)[kk]
    y <- extractMatrix(df, cells=cells)
    dim(y) <- dim(cells)
    colnames(y) <- colnames(cells)
    xlab <- substitute(y[nn], list(nn=colnames(y)[1]))
    ylab <- substitute(y[nn], list(nn=colnames(y)[2]))
    plot(NA, xlim=xlim, ylim=ylim, xlab=xlab, ylab=ylab)
    if (kk == 1)
      mtext(getFullName(df), outer=TRUE, line=1)
    stext(side=3, pos=1, sprintf("%s (n=%d)", name, nrow(y)))
    x1 <- par("usr")[2]
    y1 <- par("usr")[4]
    lines(x=c(0,x1), y=c(0,y1), lty=3, lwd=2, col="#999999")
    lines(x=c(0,0), y=c(0,y1), lty=3, lwd=2, col="#999999")
    lines(x=c(0,x1), y=c(0,0), lty=3, lwd=2, col="#999999")
    points(y, pch=pch, cex=cex, ...)
  } # for (kk ...)
  invisible(list(setsOfProbes=setsOfProbes, df=df))
}, protected=TRUE) # plotAllelePairs()