Visualize loop in hic matrix

[yancychy]

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Hi, Can pyG visulize the loops like juicebox? Thank you.

[lldelisle]

Hi, I am not sure I understand your question. pyGenomeTracks allows to display matrices and you can highlight 'loops' either by overlaying a square or by putting links below, like here: The ini file is: https://github.com/deeptools/pyGenomeTracks/blob/master/pygenometracks/tests/test_data/arcs_use_middle.ini

[yancychy]

Thanks so much. It's the square loop on hic map. I thought only arc plot is visualized under the hic map in the example page https://pygenometracks.readthedocs.io/en/latest/content/examples.html.