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higlass / higlass-manage

A utility script to manage local docker instances of HiGlass
http://docs.higlass.io
MIT License
22 stars 9 forks source link

Opacity on 2d-rectangle-domains and linear-2d-rectangle-domain track-type issue #86

Open ddepierre opened 1 year ago

ddepierre commented 1 year ago

Hi higlass team,

I have got a issue using 2d-rectangle-domains datatype, is there a way not to fill rectangles? I though Opacity 0% would do it but apparently it is still taking the score column as input of opacity, even after I set opacity to 0% Alternatively, could you add "configure series"->"Fill color"-> NULL?

image

Originally, I wanted to used the track-type: linear-2d-rectangle-domains to visualize domains, but I didn't get how to ingest it, because track-type described in https://docs.higlass.io/track_types.html#linear-2d-rectangle-domain is not an argument of ingest function, and no infos about how to prepare linear-2d-rectangle-domains datatype in https://docs.higlass.io/data_preparation.html#bedpe-like-files

I tried clodius aggregate bedfile --chromsizes-filename ./data/chrom.sizes.tsv ./data/my.bed and higlass-manage ingest ./data/my.bed.beddb --name my.bed --datatype linear-2d-rectangle-domain

No error returned but apparently my file is not ingested. if you could also help me with that please! Can I plot linear-2d-rectangle-domain from bed or it has to be from bedpe? I also tried from bedpe, but same, I can ingest it with 2d-rectangle-domain datatype (picture I attached), but does not work with linear-2d-rectangle-domain

Cheers, David