clusplot - showing variables

Question

I would like to add to a clusplot plot the variables used for pca as arrows. I am not sure that a way has been implemented (I can't find anything in the documentation).

I have produced a clusplot that looks like this:

clusters produced with clusplot

With the package princomp I can independently plot the observations in an analogous space of representation, with the variables (columns) as arrows:

enter image description here

Is there a way to do the two things at the same time, by showing the clusters and the variables of pca on the same diagram?

This question may be better suited at Cross Validated. – Ruthger Righart Apr 21 '15 at 15:37 — Ruthger Righart, Apr 21 '15 at 15:37

score 1 · Answer 1 · answered Sep 01 '16 at 22:38

I wanted to to the same thing as OP today and ended up putting pieces from clusplot and biplot together. This is the result which may be useful if you want to do the same thing:

clusplot2 <- function(dat, clustering, ...) {
    clusplot(dat, clustering, ...)

    ##  this is from clusplot.default
    pca <- princomp(dat, scores = TRUE, cor = (ncol(dat) != 2))

    ##  this is (adapted) from biplot.princomp 
    directions <- t(t(pca$loadings[, 1:2]) * pca$sdev[1:2]) * sqrt(pca$n.obs)

    ##  all below is (adapted) from biplot.default
    unsigned.range <- function(x) c(-abs(min(x, na.rm = TRUE)), 
                                    abs(max(x, na.rm = TRUE)))
    x <- predict(pca)[, 1:2]
    y <- directions
    rangx1 <- unsigned.range(x[, 1L])
    rangx2 <- unsigned.range(x[, 2L])
    rangy1 <- unsigned.range(y[, 1L])
    rangy2 <- unsigned.range(y[, 2L])
    xlim <- ylim <- rangx1 <- rangx2 <- range(rangx1, rangx2)
    ratio <- max(rangy1/rangx1, rangy2/rangx2)
    par(new = T)
    col <- par("col")
    if (!is.numeric(col)) 
        col <- match(col, palette(), nomatch = 1L)
    col <- c(col, col + 1L)
    cex <- rep(par("cex"), 2)
    plot(y, axes = FALSE, type = "n", xlim = xlim * ratio, ylim = ylim * 
             ratio, xlab = "", ylab = "", col = col[1L])
    axis(3, col = col[2L])
    axis(4, col = col[2L])
    box(col = col[1L])
    text(y, labels = names(dat), cex = cex[2L], col = col[2L])
    arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[2L], 
           length = 0.1)
}

############################################################

library(cluster)

dat <- iris[, 1:4]

clus <- pam(dat, k = 3)
clusplot2(dat, clus$clustering, main = "Test")

Of course there is much room for improvement (as this is just copied together) but I think anyone can easily adapt it if needed.

If you wonder why the arrows (loadings * sdev) are scaled with 0.8 * sqrt(n): I have absolutely no idea. I would have plotted loadings * sdev which should resemble the correlation between the principal components and the variables but this is how biplot does it.

Anyway, this should produce the same arrows as biplot.princomp and use the same pca as clusplot which was the primary goal for me.

clusplot - showing variables

1 Answers1