It's not so much a problem, as not working the way you expected.
cluster:::plot.partition is used to do the plotting. If you look at the code
for this you can see the difficulty in putting every possible permutation into
the code. If for example you want the silhouette plot to be red using col =
"red" is not intuitive as the cluster plot (which comes up first) has more than
one colour. If you have a look at methods(plot) (assuming that you have loaded
the cluster package) you will see that there is a specific piece of code in the
form of plot.silhouette. It has an asterisk next to it so you need to use
cluster:::plot.silhouette to see the code. It has what you need.
args(cluster:::plot.silhouette)
> function (x, nmax.lab = 40, max.strlen = 5, main = NULL, sub = NULL,
xlab = expression("Silhouette width " * s[i]), col = "gray",
do.col.sort = length(col) > 1, border = 0, cex.names = par("cex.axis"),
do.n.k = TRUE, do.clus.stat = TRUE, ...)
data(ruspini)
pr4 <- pam(ruspini, 4)
si <- silhouette(pr4)
plot(si,col = "red")
The issue is that whenever code is written there is always a choice as to what
functionality is put in place. Just because something can be done, does not
mean it will or in some cases should be done. In this case the help for
plot.partition notes that "For more flexibility, use 'plot(silhouette(x),
...)', see 'plot.silhouette'."
Tom
Thanks for that I found out something I will find useful in the future.
> -----Original Message-----
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of A. Mani
> Sent: Tuesday, 28 June 2005 4:30 AM
> To: [email protected]
> Subject: [R] A. Mani : colours in Silhouette
>
>
> Hello,
> In cluster analysis with cluster, how does one colour
> the silhouette
> plots ? For example in using pam. There seems to be some
> problem there.
> Everything else can be coloured.
>
> Thanks,
>
> A. Mani
> Member, Cal. Math. Soc
>
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