Hi all, here's a quick reply to an old thread: I also have the feeling heatmap.2 row ordering without using a dendrogram does not work (even with R 2.9 & latest Bioc). # My workaround is to change the order of rows in the gene expression input matrix toPlot = toPlot[order(rownames(toPlot)),] # then I run heatmap.2 while telling it not to reorder rows... heatmap.2(toPlot, Rowv=FALSE, dendrogram="none") best, Yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html On September 4th 2008, Sean Davis wrote: > You need to at least turn off row dendrograms; you cannot arbitrarily > reorder a dendrogram. However, I remember that there were some bugs > with heatmap.2 in the past that precluded the row ordering from > working correctly (i.e., vector order if dendrogram was not used). I > haven't checked recently to see if that is still the case. > > Hope that helps. > > Sean > Iain Gallagher wrote; >> Hi List. >> >> I have question I hope someone can help me with. I have a matrix of >> gene expression results and I would like to >> generate a heatmap with each gene plotted in the order of a vector >> (specifically a biological parameter >> that all the genes co vary with). I've been wrestling with this for >> a couple of days now and I'm not sure my >> approach is right. >> >> z_mat is my matrix - samples in columns and genes in rows. >> >> max_resp is my biological parameter - a vector of values (1 for >> each subject). >> >> What I'd like is a gradient of expression for each gene >> (ideally)... the expression values do generally >> increase as max_resp increases. But I can't seem to get this and my >> heatmaps seem messier than they should be. >> >> Is there a way to order the rows (gene expression values) of the >> heatmap to reflect the order of the max_resp vector? >> >> For example I've tried: >> >> max_order<-order(change_data[,2]) >> >> to set a vector reflecting the order of the max_resp parameter from >> lowest to highest >> >> heatmap.2(z_mat, col=heatcols, Colv=max_order, labCol=change_data[, >> 2][max_order]) >> >> but the labeling (labCol) is not in order (i.e. max_order) and the >> colour gradient does not reflect my data >> (i.e. generally good correlation of gene expression and max_resp). >> >> My understanding of the heatmap.2 help is that setting Colv (or >> Rowv) to a vector reorders the dendrogram to >> the vector order... my understanding is likely flawed. >> >> Could someone give me some advice? >> >> Thanks. >> >> Iain >> >> sessionInfo() >> R version 2.7.2 (2008-08-25) >> i486-pc-linux-gnu >> >> locale: >> LC_CTYPE >> = >> en_GB >> .UTF >> -8 >> ;LC_NUMERIC >> = >> C >> ;LC_TIME >> = >> en_GB >> .UTF >> -8 >> ;LC_COLLATE >> = >> en_GB >> .UTF >> -8 >> ;LC_MONETARY >> = >> C >> ;LC_MESSAGES >> = >> en_GB >> .UTF >> -8 >> ;LC_PAPER >> = >> en_GB >> .UTF >> -8 >> ;LC_NAME >> = >> C >> ;LC_ADDRESS >> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] RColorBrewer_1.0-2 gplots_2.6.0 gdata_2.4.2 >> gtools_2.5.0