BandageNG icon indicating copy to clipboard operation
BandageNG copied to clipboard

how to color a graph

Open Overcraft90 opened this issue 1 month ago • 1 comments

Hi I'm working with a pangenome built with PGGB, it's made up by five human individuals plus two references (CHM13 and GRCh38). What I wish to do is to attribute a color to paths based on those genomes (if possible) and, specifically, so that the graph's components are colored based on their geographic region of origin. E.g. AFR=yellow, EUR=blue, EAS=red etc.

Let me know how should I prepare the .csv to achieve this, I imagine I would need a column with samples' names and haplotypes another with the colors, and maybe one with the population group? It's the first time I'm doing this, so I'm trying to understand how it can be achieved. To be noted, I named haplotypes' FASTA according to the fastix convention as follow:

<sample>#haplotype_number (either 1 or 2, 0 for references)#chr_num

Thanks in advance!

Overcraft90 avatar Nov 15 '25 15:11 Overcraft90

Unfortunately, I have not enough time to revamp the documentation. Here is the old one from Bandage: https://github.com/rrwick/Bandage/wiki/CSV-labels

Essentially you can label either nodes or whole paths (if your GFA contains them).

Alternatively, you can use GFA tags for labelling akin to rGFA.

asl avatar Nov 16 '25 21:11 asl