Entering edit mode
On 5/31/06 2:25 AM, "Ron Ophir" <ron.ophir at="" weizmann.ac.il=""> wrote:
> 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)
Couldn't have (and, indeed, didn't) said it better myself.
Sean
>>>> 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