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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=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 [[alternative HTML version deleted]]

On Thu, Sep 4, 2008 at 5:29 PM, Iain Gallagher <iaingallagher at="" btopenworld.com=""> 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. 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