Hi Aaron,

Is there any way to run plotPlain in diffHic package using output from HiC-Pro? saying using a precomputed HiC matrix from HiC-Pro, and a bed file with bin coordinates. Thanks.

The easiest approach is to take the BAM files produced by HiC-Pro, use preparePairs to generate HDF5 files, and then use those files in plotPlaid. Trying to do so from a precomputed matrix is somewhat confusing as you'll have to pretend that your bins are fragments in order to use plotPlaid.

Alternatively, I guess you could use plotDI for plotting instead. This requires that you generate an InteractionSet from the HiC-Pro contact matrix, and then pretend the normalised intensities are log-fold changes. It should be trivial to construct a ContactMatrix object from the matrix and coordinates; you can then use the deflate method to easily convert this to an InteractionSet.