[R] Self-Organizing Map analysis
Hans W. Borchers
hwborchers at gmail.com
Wed Mar 4 09:13:09 CET 2009
glaporta <glaporta <at> freeweb.org> writes:
>
> Dear list,
> I read the SOM package manual but I don't understand how to perform (for
> example) 1) the SOM analysis on Iris data 2) with a visualization similar to
> that of figure 7 in
> http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf
In R, I used the following calls to create SOM maps similar to the ones in the
literature (I don't find the SOM toolbox figures particularly inspiring):
----
library("class")
data(iris)
n <- 10
sg <- somgrid(n, n, "rectangular")
df.som <- batchSOM(df, sg, c(4,4,3,3,2,2,1,1))
windows(record=TRUE)
for (i in 1:ncol(df)) {
xy <- matrix(df.som$codes[,i], n, n)
image(xy)
contour(xy, add=T)
grid(col="gray")
}
----
Of course, there are not enough Iris data to generate a reasonable SOM grid. At
least n <- 30 is needed for a nice graph, and that means at least 1000 data
points.
Using a Binhex grid instead of a rectangular one will result in diagrams similar
to those from the SOM toolbox. But then the 'image' call has to be a bit
prepared for this.
Regards, Hans Werner
> Any suggestion? Thanks in advance,
> Gianandrea
More information about the R-help
mailing list