<p>I am using NGSPLOT to generate heatmaps of a couple of TF&#39;s, but the output only gives me the same color for each heatmap. I was wondering if it was possible to generate the heatmaps with different colors for each heatmap to differentiate between them easier.</p>

<p>I&#39;ve looked everywhere in the documentation, and it appears it should be possible (based on some images in the ngsplot paper) but I can&#39;t seem to figure out how. Does anyone have any idea?</p>

You can generate something like this figure 2b in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220495/figure/f2/ using [deepTools][1]. You simply specify the colorMap that you want.

 [1]: http://deeptools.readthedocs.org/en/latest/content/tools/plotHeatmap.html