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