Deeptools plotHeatmap - Maintain Order of Input BED file

Question

[cpak1981]

Hi:

I was wondering how I can maintain the order of my input bed file when plotting epigenetic markers using deeptools plotheatmap. If I set '--sortRegions keep' in computeMatrix and '--sortRegions no' in plotHeatmap, will this preserve the order of entries in my bed file in the resulting plot? Also, if I am plotting multiple epigenetic markers and want to the preserve the order of entries in my bed file for all plots, do I need to additionally specify '--sortUsing'?

Answer 1

[Devon Ryan]

Yes, if you use --sortRegions keep in computeMatrix and --sortRegions no in plotHeatmap then the order will match your input file(s).

You don't need --sortUsing at all. When one sorts the output (e.g., by mean), then the mean across all samples is used to determine the sorting. The --sortUsing option allows you to sort according to the signal in a single sample.