Hi, there is a problem with the plotHeatmap tool in deepTools in that it sometimes incorrectly assigns data as missing (and therefore draws black on the heatmap) when the data is actually not missing. For example, if I plot 999 genes, it plots them correctly, but if I just add one more gene, to make it 1000, suddenly the tool draws more black lines at the right of the heatmap, as though some genes are much shorter than they really are. Please see the first two attached pictures of 999 and 1000 genes – it’s more evident when you zoom in and go back and forth from one to the other. It becomes more of a problem when I plot more genes, like 10 000 (please see the third picture). In addition, if I select the option to save the heatmap values, they are reported correctly with any number of genes, it is only the actual heatmap drawing that is incorrect.
In the original deepTools (the one that was run from Germany, I think), this problem did not exist, and I could plot even 10 000 genes correctly. Please compare the attached pictures 3 and 4 – it’s the same data, but picture 4 was plotted from the original deepTools server a few months ago. Picture 4 is how it should look like, all the black lines in picture 3 are wrong, as there are not so many short genes in the human genome.
Thank you!
