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MDSplot <- function(rf, fac, k=2, palette=NULL, pch=20, ...) {
if (!inherits(rf, "randomForest"))
stop(deparse(substitute(rf)), " must be a randomForest object")
if(is.null(rf$proximity))
stop(deparse(substitute(rf)), " does not contain a proximity matrix")
op <- par(pty="s")
on.exit(par(op))
rf.mds <- stats::cmdscale(1 - rf$proximity, eig=TRUE, k=k)
colnames(rf.mds$points) <- paste("Dim", 1:k)
nlevs <- nlevels(fac)
if (is.null(palette)) {
palette <- if (requireNamespace("RColorBrewer", quietly = TRUE) && nlevs < 12)
RColorBrewer::brewer.pal(nlevs, "Set1") else rainbow(nlevs)
}
if (k <= 2) {
plot(rf.mds$points, col=palette[as.numeric(fac)], pch=pch, ...)
} else {
pairs(rf.mds$points, col=palette[as.numeric(fac)], pch=pch, ...)
}
invisible(rf.mds)
}
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