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AmpliconSuite / CoRAL

Reconstruction of focal amplifications with long reads
BSD 3-Clause "New" or "Revised" License
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Custom plotting #6

Closed jluebeck closed 6 months ago

jluebeck commented 6 months ago

Adds ability to set a --region chrom:pos1-pos2 when plotting the graph.

kyzhu commented 6 months ago

Hi @jluebeck, Do you think it's better to use chr_idx in global_names.py (just in consistent with other files) instead of an explicit sorting?

jluebeck commented 6 months ago

Hi @kyzhu, the strategy implemented in the plotting code for this branch is more general than hardcoding the chromosome names, and would allow you to easily support other species (e.g. mm10). I think you will probably want to switch everything over to my sorting method eventually. I am not really inclined to switch the plotting code back to hardcoded names. Feel free to move my sorting function to a more centralized library file though.

I can make a separate PR tomorrow if you'd like that switches all chromosome sorting to the general method.

kyzhu commented 6 months ago

I got it and that makes sense. I will merge this PR then