For parameter options please see the pyGenomeTracks documentation.
The hicPlotTADs output is similar to a genome browser screenshot that besides the usual genes and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified in a configuration file. Once the track file is ready, hicPlotTADs can be used as follows:
$ hicPlotTADs --tracks tracks.ini --region chrX:99,974,316-101,359,967 \ -t 'Marks et. al. TADs on X' -o tads.pdf
The following is a template for the configuration file which is based on .ini configuration files. Each track is defined by a section header (for example [hic track]), followed by parameters specific to the section as color, title, etc. For details please see the documentation of pyGenomeTracks.
$ hicPlotTADs --tracks hic_track.ini -o hic_track.png --region chrX:2500000-3500000
[x-axis] where = top [hic matrix] file = hic_data.h5 title = Hi-C data # depth is the maximum distance plotted in bp. In Hi-C tracks # the height of the track is calculated based on the depth such # that the matrix does not look deformed depth = 300000 transform = log1p file_type = hic_matrix [tads] file = domains.bed file_type = domains border_color = black color = none # the tads are overlay over the hic-matrix # the share-y options sets the y-axis to be shared # between the Hi-C matrix and the TADs. overlay_previous = share-y [spacer] [bigwig file test] file = bigwig.bw # height of the track in cm (optional value) height = 4 title = ChIP-seq min_value = 0 max_value = 30