R/principal.curve.pairs2.R

In aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

setMethodS3("pairs2", "principal.curve", function(fit, pch=19L, cex=0.8, fitCol="red", fitLwd=2, fitLty=1L, xlim=NULL, ylim=xlim, lower.panel=NULL, ...) {
  r <- range(c(fit$s, fit$Y), na.rm=TRUE)

  # Argument 'xlim' & 'ylim':
  if (is.null(xlim)) {
    xlim <- r
  }
  if (is.null(ylim)) {
    ylim <- r
  }

  hasData <- !is.null(fit$Y)

  nbrOfVars <- ncol(fit$s)
  layout(matrix(seq_len((nbrOfVars-1)^2), nrow=nbrOfVars-1L, ncol=nbrOfVars-1L, byrow=TRUE))
  par(mar=c(3,3,1,1)+0.1)
  for (rr in seq_len(nbrOfVars)) {
    if (rr == nbrOfVars)
      next
    for (cc in seq_len(nbrOfVars)) {
      if (cc < rr) {
        plot.new()
      } else if (cc == rr) {
      } else {
        plot(NA, xlim=xlim, ylim=ylim, xlab="", ylab="")
        abline(a=0, b=1, lty=3L, col="#999999", lwd=2)
        if (hasData) {
          y <- fit$Y[,c(cc,rr),drop=FALSE]
          points(y, pch=pch, cex=cex, ...)
        }

        if (fitLwd > 0) {
          y <- fit$s[,c(cc,rr),drop=FALSE]
          o <- order(y[,1L,drop=TRUE])
          y <- y[o,,drop=FALSE]
          lines(y, col=fitCol, lwd=fitLwd, lty=fitLty)
        }
      }
    } # for (cc ...)
  } # for (rr ...)
}) # pairs2()