From reading through documentation for plotHeatMap, I am a bit confused as to whether the subplots for each sample share the same row ordering, or whether rows are clustered independently in each subplot. Specifically, documentation for the --sortUsingSamples option states (bold text my addition):
List of sample numbers (order as in matrix), that are used for sorting by --sortUsing, no value uses all samples, example: --sortUsingSamples 1 3"
This seems to imply that the row order is set based on global clustering of all samples by default, but leaves a bit too much room for interpretation for me to be confident that I know what is happening under the hood.
I know that it is possible to order rows externally and use --sortRegions no to retain that ordering in the final plot, or to use any single sample or combination of samples with --sortUsingSamples such that rows in all plots are ordered relative to the given reference(s). I just want to be sure I understand what is happening by default and am hoping someone can verify.
Thanks in advance!
