Hello, we had the same idea Vincent had. We generate a dendrogram and use that for the columns. The variable experimentgroups has the default settings. A special feature is that we allow multiple groups of "indistinguishable" patients. The distances 0 within such a group and neighboured groups have distances of 1. cat("Please enter sizes of groups for distance calculation or (defaut: ",paste(experimentgroups,sep=" "),"):\n") groups <- scan(what=integer(0)) #vector containing number of members for each group if (length(groups)==0) { groups<-experimentgroups } dend<-rep(0,sum(groups)) last<-0 for (i in 1:length(groups)) { dend[(last+1):sum(groups[1:i])]<-rep(i,groups[i]) last<-sum(groups[1:i]) } print(dend) dend<-as.dendrogram(hclust(dist(dend))) print(dend) hv<-heatmap(dat2, Colv=dend, Henning and Steffen Vincent Carey 525-2265 wrote: >>I have four experiments (two dye swaps) and this is the original order: >> >> >>>colnames(mav) >>> >>> >>[1] Cy3="Cancer" Cy5="Normal" Cy3="Cancer" Cy5="Normal" Cy3="Normal" >>Cy5="Cancer"Cy3=" Normal" Cy5="Cancer" >> >>I want to get a heatmap of the top 30 expressed genes but ordered by >>cancerous vs. normal tissue. >> >> >>>hv <- heatmap(mav[genes %in% topgenes$Name,],col=RGcol) >>>title("Heatmap of Top 30 genes") >>>str(hv) >>> >>> >>List of 2 >> $ rowInd: int [1:30] 5 8 30 13 7 27 19 21 25 26 ... >> $ colInd: int [1:8] 4 3 8 7 1 5 2 6 >> >>No matter what I do, the columns are reordered. Furthermore, if I set Colv=F >>the heatmap stays the same but the ordering changes. >> >> > >I believe this needs to be taken up with the R developers. >I have not seen how to suppress reordering short of going >into the source and commenting out the reordering step. > >A non-invasive workaround is to create a dendrogram that corresponds >to the order you desire and to use that as the argument value. >In my case, I clustered 1:n, reordered the result a little >bit and I was able to subvert the heatmap behavior. Sorry for >the vague account -- it was an emergency operation and the >materials are not ready to hand. > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > -- Steffen M?ller, PhD Universit?t Rostock Institut f?r Immunologie Proteom-Zentrum Rostock Joachim-Jungius-Str. 9 D-18059 Rostock steffen.moeller@med.uni-rostock.de +49 381 4059 684 Fax: -686