Hi,
I just came across the latest update on the vignette of "DESeq". I really like the new additions on visualizations particularly the visualization of expression data from genes. In my rna-seq experiment I have two conditions/treatments and three biological replication per treatment. I did the differential expression analysis and variance stabilized data using "DESeq". I want to use the VSD for generating heat map of top DE genes. I am using heatmap.2. I am able to generate a good heat map. However , I want to place an horizontal bar (below the vertical dendrogram) using 'ColSideColors' function of heat map2. I have generated the heatmap with the dendrogram of sample data (three biological replicates ie C1,C2,C3,S1,S2,S3;  C=control; S=stress) on the top (vertical) of map. On the horizontal bar (below the vertical dendrogram) I want to have two colours one for each of the two treatments. I am able to add one colour to each sample using 'rainbow' and 'heat.colors' functions but I want to use only two colours one for each of the two conditions.

Could anyone please show me how to do this.

Thank you.
Bala

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