[BioC] [heatmap] different distance functions for columns and for rows

[Ron Ophir]

I see. I missed it. You mean something like this

x<-matrix(rnorm(1000,10,2),100,100)
hc<-as.dendrogram(hclust(dist(x,method="euclidean")))
hr<-as.dendrogram(hclust(as.dist(cor(x,method="pearson"))))
x11();hv <- heatmap(x,Rowv=hr,Colv=hc)

Thanks,
Ron


>>> Sean Davis <sdavis2 at mail.nih.gov> 30/05/2006 22:02:16 >>>



On 5/30/06 3:56 PM, "Ron Ophir" <ron.ophir at weizmann.ac.il> wrote:

> I would like to run clustering on columns (samples) and rows (genes)
and
> get a plot similar to the output of heatmap(). However I would like
to
> apply euclidean distance to samples and pearson distance to genes.
> Is it possible to do it with heatmap(). If not, is there other
function
> that can do it?

Ron,

You can pass Rowv and Colv dendrogram objects, as output by hclust,
for
example.  By doing so, you can use different distance functions (or
even
different clustering algorithms) for the rows and columns.

Sean