scoreplot: Plot discriminant function scores, with various identification

Description

There is provision for the plottting of two sets of scores on the same graph, possibly with different classifying factors. The function is designed for use with output from cvscores() or from simulateScores().

Usage

scoreplot(scorelist, plot.disc = 1:2, xlab = NULL, ylab = NULL, params = NULL,
          circle = NULL, cl.circle = NULL, circle.pos = c(1, 1), adj.circle = 1,
          adj.title = 0.5, join.legends = TRUE, prefix.title = "", cex.title = 1,
          ratio = 1, plot.folds = FALSE, ...)

Value

A graph is plotted.

Arguments

scorelist: list, with elements scores (a matrix of scores) cl (a classifying factor), other (optional, a further sets of scores), cl.other (a a classifying factor for other, optional) and nfeatures (optional, used to label the graph)
plot.disc: choice of columns of scorelist to plot
xlab: label for x-axis
ylab: label for y-axis
params: List, with optional elements (lists) points, other, circle and legend. Allowed list elements for points and other are cex, lwd, pch and col. For circle they are cex, lwd and col. For legend, they are cex and cex.other
circle: identifies points that are to be circled
cl.circle: different colors may be used for different points, according to levels of cl.circle
circle.pos: This is a vector of length 2, that specifies where to place the legend information for the circling of points. Possibilities are c(0,0) (left, below), c(1,1) (right, above), etc.
adj.circle: controls positioning of circle legend
adj.title: controls positioning of title
join.legends: logical; should legends for points and other be combined?
prefix.title: prefix, to place before title
cex.title: cex for title
ratio: y-scale to x-scale ratio for graph
plot.folds: Plot individual fold information, comparing projected training scores with their projections onto the global space. This is not at present implemented
...: Other parameters to be passed to eqscplot()

Author

John Maindonald

Examples

Run this code

## Use first 500 rows (expression values) of Golub, for demonstration.
data(Golub)
data(golubInfo)
attach(golubInfo)
miniG.BM <- Golub[1:500, BM.PB=="BM"]  # 1st 500 rows only
cancer.BM <- cancer[BM.PB=="BM"]
miniG.cv <- cvdisc(miniG.BM, cl=cancer.BM, nfeatures=1:10,
                    nfold=c(3,1))
miniG.scores <- cvscores(cvlist=miniG.cv, nfeatures=4,
                         cl.other=NULL)
subsetB <- (cancer=="allB") & (tissue.mf %in% c("BM:f","BM:m","PB:m"))
tissue.mfB <- tissue.mf[subsetB, drop=TRUE]
scoreplot(scorelist=miniG.scores, cl.circle=tissue.mfB,
       circle=tissue.mfB%in%c("BM:f","BM:m"),
       params=list(circle=list(col=c("cyan","gray"))),
       prefix="BM samples -")
detach(golubInfo)

## The function is currently defined as
  function(scorelist, plot.disc=1:2,
           xlab=NULL, ylab=NULL, params=NULL,
           circle=NULL, cl.circle=NULL, circle.pos=c(1,1),
           adj.circle=1,
           adj.title=0.5, join.legends=T, prefix.title="Golub data - ",
           cex.title=1.0, ratio=1, plot.folds=FALSE, ...){
    library(MASS)
    combine.params <-
      function(params=list(circle=list(col=c("cyan","gray")))){
        default.params=list(points=list(cex=1, lwd=1.25, pch=1:8, col=1:8),
          other=list(cex=0.65, lwd=1.25, pch=13:9, col=c(6:8,5:1)),
          circle=list(cex=2, lwd=1, pch=1.75, col="gray40"),
          legend=list(cex=1, cex.other=1))
        nam <- names(params)
        if(!is.null(nam))
          for(a in nam){
            nam2 <- names(params[[a]])
            for(b in nam2)default.params[[a]][[b]] <- params[[a]][[b]]
          }
        default.params
      }
    params <- combine.params(params=params)
    cl <- scorelist$cl
    cl.other <- scorelist$cl.other
    if(!is.null(cl.other)) cl.other <- factor(cl.other)
    nfeatures <- scorelist$nfeatures
    if(length(plot.disc)==2){
      n1 <- plot.disc[1]
      n2 <- plot.disc[2]
      if(is.null(xlab))xlab <- paste("Discriminant function", n1)
      if(is.null(ylab))ylab <- paste("Discriminant function", n2)
    } else stop("plot.disc must be a vector of length 2")
    if(!is.factor(cl))cl <- factor(cl)
    levnames <- levels(cl)
    fitscores <- scorelist$scores
    other.scores <- scorelist$other
    ngp <- length(levnames)
    n1lim <- range(fitscores[,n1])
    n2lim <- range(fitscores[,n2])
    if(!is.null(cl.other)){
      n1lim <- range(c(n1lim, other.scores[,n1]))
      n2lim <- range(c(n2lim, other.scores[,n2]))
      levnum <- unclass(cl.other)
      levnames.other <- levels(cl.other)
      intlev.other <- unclass(cl.other)
      ngp.other <- length(levels(cl.other))
    }
    n1 <- plot.disc[1]; n2 <- plot.disc[2]
    intlev <- unclass(cl)
    oldpar <- par(lwd=1)
    on.exit(par(oldpar))
    eqscplot(n1lim, n2lim, type="n",
             xlab=xlab, ylab=ylab, ratio=ratio, ...)
    with(params$points,
         points(fitscores[,n1], fitscores[,n2], col=col[intlev],
                pch=pch[intlev], cex=cex, lwd=lwd))
    if(!is.null(cl.other))
      with(params$other,
           points(other.scores[,n1], other.scores[,n2],
                  pch=pch[intlev.other],
                  col=col[intlev.other],
                  cex=cex, lwd=lwd))
    if(!is.null(cl.circle)){
      cl.circle <- factor(cl.circle[circle])
      lev.circle <- levels(cl.circle)
      with(params$circle,
           points(fitscores[circle, n1], fitscores[circle,n2], pch=pch,
                  cex=cex, col=col[unclass(cl.circle)], lwd=lwd))
    }
    par(xpd=TRUE)
    chw <- par()$cxy[1]
    chh <- par()$cxy[2]
    par(lwd=1.5)
    ypos <- par()$usr[4]
    xmid <- mean(par()$usr[1:2])
    top.pos <- 0
    mtext(side=3, line=(top.pos+1), paste(prefix.title,
            nfeatures, "features"), cex=cex.title, adj=adj.title)
    ypos.legend <- ypos+(top.pos-0.45)*chh*0.8

    if(join.legends&!is.null(cl.other)){
      leg.info <- legend(xmid, ypos.legend, xjust=0.5, yjust=0, plot=FALSE,
                         x.intersp=0.5, ncol=ngp, legend=levnames,
                         pt.lwd=params$points$lwd,
                         pt.cex=params$points$cex,
                         cex=params$legend$cex,
                         pch=params$points$pch)
      legother.info <- legend(xmid, ypos.legend, xjust=0.5, yjust=0,
                              plot=FALSE, x.intersp=0.5,
                              ncol=ngp.other, legend=levnames.other,
                              pt.lwd=params$other$lwd,
                              pt.cex=params$other$cex,
                              cex=params$legend$cex.other,
                              pch=params$other$pch)
      leftoff <- 0.5*legother.info$rect$w-0.5*chw
      rightoff <- 0.5*leg.info$rect$w+0.5*chw
      ypos.other <- ypos.legend
    }
    else {
      leftoff <- 0
      rightoff <- 0
      ypos.other <- ypos+(top.pos-1.5)*chh*0.8
    }
    legend(xmid-leftoff, ypos.legend, xjust=0.5, yjust=0,
           bty="n", pch=params$points$pch,
           x.intersp=0.5, col=params$points$col, ncol=ngp,
           legend=levnames,
           pt.lwd=params$points$lwd,
           pt.cex=params$points$cex,
           cex=params$legend$cex)
    par(lwd=1)
    if(!is.null(cl.other))
      lego.info <- legend(xmid+rightoff, ypos.other, xjust=0.5, yjust=0,
                          pch=params$other$pch, x.intersp=0.5,
                          col=params$other$col, ncol=ngp.other,
                          pt.lwd=params$other$lwd,
                          pt.cex=params$other$cex,
                          legend=levnames.other,
                          cex=params$legend$cex.other,
                          bty="n")
    if(!is.null(cl.other)&join.legends)
      text(lego.info$rect$left+c(0.4*chw,lego.info$rect$w-0.25*chw),
           rep(ypos.other,2)+0.8*chh, labels=c("(",")"),
           cex=params$legend$cex,
           lwd=params$legend$lwd, bty="n")
    par(lwd=params$circle$lwd)
    if(!is.null(cl.circle))if(lev.circle[1]!=""){
      pch.circle <- params$circle$pch
      xy <- par()$usr[circle.pos+c(1,3)]
      legend(xy[1], xy[2],
             xjust=adj.circle[1], yjust=circle.pos[2], bty="n", x.intersp=0.5,
             pch=rep(pch.circle,length(lev.circle)), col=params$circle$col,
             ncol=1, legend=lev.circle, cex=0.85, pt.cex=1.5)
    }
    par(lwd=1, xpd=FALSE)
    if(plot.folds){
      mtext(side=1, line=1.25, "Discriminant function 1", outer=T)
      mtext(side=2, line=1.25, "Discriminant function 2", outer=T)
    }
  }