[R] dissimilarity matrices

[Gavin Simpson]

On Thu, 2006-11-09 at 17:50 +0000, Kris Lockyear wrote:
> Dear All,
> 
> I have a dissimilarity matrix which I happily convert to a distance object 
> by running:
> 
> X <- as.dist(Y)
> 
> and I can happily now run either hclust(X) or agnes(X).
> 
> So that the various bits of output are labelled correctly I would dearly 
> like to be able to give names to the columns and rows of X, as would happen 
> if I ran:
> 
> mydata<-read.table("clipboard",header=T)
> mydata2<-t(mydata)
> mydists<-dist(mydata2)

I assume Y doesn't have column/row names then? So give Y some col/row
names before you convert it to a dist object:

> mat <- matrix(seq(0.1, 0.9, by = 0.1), ncol = 3)
> diag(mat) <- 0
> mat
     [,1] [,2] [,3]
[1,]  0.0  0.4  0.7
[2,]  0.2  0.0  0.8
[3,]  0.3  0.6  0.0
> distmat <- as.dist(mat)
> distmat
    1   2
2 0.2
3 0.3 0.6
> rownames(mat) <- colnames(mat) <- LETTERS[1:3]
> distmat <- as.dist(mat)
> distmat
    A   B
B 0.2
C 0.3 0.6

or you can modify the "Labels" attribute of your object X, *after* you
have done as.dist(Y), e.g. following on from the above example:

> attr(distmat, "Labels") <- paste("Samp", 1:3, sep = "")
> distmat
      Samp1 Samp2
Samp2   0.2
Samp3   0.3   0.6

HTH

G

> 
> Many thanks for your help.
> 
> Best wishes, Kris Lockyear.

-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson                     [t] +44 (0)20 7679 0522
ECRC                              [f] +44 (0)20 7679 0565
UCL Department of Geography
Pearson Building                  [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street
London, UK                        [w] http://www.ucl.ac.uk/~ucfagls/
WC1E 6BT                          [w] http://www.freshwaters.org.uk/
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%