Dear all,
I am making heatmaps for enrichment of certain histone marks in my ChIP-Seq data with NGSPlot. The default colors in the heatmaps that the command ngs.plot.r creates are red (for the histone mark or TF binding) and white (background). However, I would like to use a different color scheme to make the contrast between my histone mark and the background clearer; e.g., yellow for the histone mark enrichment and blue for the background. From the documentation at https://github.com/shenlab-sinai/ngsplot this seems to be possible looking at some of their heatmaps. However, they don't elaborate upon the details of how to specify your own colors for the heatmap. I have been trying the -CO option but it continues to give me errors. Can someone please help me?
Many thanks, Cemil
Check the Heatmap parameters in Arguments101 wiki.