Difference between heatmap and clustermap
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I am trying to generate a heatmap for gene expression data in the matrix "foldchange". I notice that heatmap(log2(foldchange)) produces a heatmap which looks mostly black.
But when I use clustermap on the same data, I get a heatmap (with dendogram) where the colors are either mostly green/red. I don't understand why the two images are different when both heatmap and clustermap functions generate a heatmap. Does clustermap scale the data differently?
Lucio Cetto on 18 Oct 2011
clustergram automatically standarizes the data in order to maximize the usage of the colormap. You may also alter the dynamic range of the HeatMap by using the DisplayRange and Symmetric properties.