HiCPlotmatrix

[DakeshiKitano]

Dear authors,

Greetings and kudos to you for HiCExplorer!

I tried to plot all mouse chromosomes of .h5 file via HiCPlotMatrix using these parameters (chromosomeOrder, -log1p). The .h5 file was a comparative matrix of log2ratio of mutant over wild-type.

1. Does plotting a single chromosome show contact frequency of that chromosome within itself? Or does it show contact frequency of regions from that chromosome versus the whole genome (versus all other chromosomes)?
2. Also, when all chromosomes are depicted, will they show a contact matrix of interactions e.g. chr1 vs chr 2, when all the chromosomes were listed via chromosomeOrder (as shown an exemplary figure attached to this issue)

Best regards,
Daulet.