Dear all, I have been using R for a short time now and I am having a little difficulty with the following. Whilst I am able to generate one row of ColSideColors above my heatmap, I would like to generate 2 ColSideColors each representing different information. So far I have: #the column one from my headers file is used as ColSideColors mycols2 <- as.character(as.numeric(headers$one)); #I would also like to present this column (two) aswell, but do not know how.. mycols3<-as.character(as.numeric(headers$two)); heatmap(mymatrix,ColSideColors = mycols2,col= greenred(256)); How can I incorporate mycols3 into the heatmap function as well? I am thinking it must be a syntax issue which I am not too familiar with yet. Thank you to anyone who can help me

Dear Sabah, have a look at this: http://tolstoy.newcastle.edu.au/R/e2/help/07/09/25712.html there is a code example, I repeat it here for your convenience: library("lattice") library("latticeExtra") hc1 = hclust(dist(USArrests, method = "canberra")) hc1 = as.dendrogram(hc1) ord.hc1 = order.dendrogram(hc1) hc2 = reorder(hc1, state.region[ord.hc1]) ord.hc2 = order.dendrogram(hc2) region.colors = trellis.par.get("superpose.polygon")$col levelplot(t(scale(USArrests))[, ord.hc2], scales = list(x = list(rot = 90)), colorkey = FALSE, legend = list(right = list(fun = dendrogramGrob, args = list(x = hc2, ord = ord.hc2, side = "right", size = 10, size.add= 0.5, add = list( rect = list(col = "transparent", fill = region.colors[state.region]), rect = list(col = "transparent", fill = region.colors[rev(state.region)])), type = "rectangle")))) Generally, the heatmap function from the base package is quite inflexible, and I doubt that it would be easy or worthwhile to make it do what you propose. The suggestion that Deepayan is making above will require a certain amount of investment of your time in understanding how the lattice graphics package works, but it is worth it! Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Sabah khalid ha scritto: > Dear all, > > I have been using R for a short time now and I am having a little difficulty > with the following. Whilst I am able to generate one row of ColSideColors > above my heatmap, I would like to generate 2 ColSideColors each representing > different information. > > So far I have: > > #the column one from my headers file is used as ColSideColors > mycols2 <- as.character(as.numeric(headers$one)); > #I would also like to present this column (two) aswell, but do not know > how.. > mycols3<-as.character(as.numeric(headers$two)); > > heatmap(mymatrix,ColSideColors = mycols2,col= greenred(256)); > > How can I incorporate mycols3 into the heatmap function as well? I am > thinking it must be a syntax issue which I am not too familiar with yet. > > Thank you to anyone who can help me > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor