Pangenome presence absence viz ?

[colindaven]

Dear devs,

I'm interested in visualizing a pangenome matrix from odgi pavs in JBrowse1.

Maybe someone has made something like this viewer, panache as an example.

https://www.appliedbioinformatics.com.au/wheat_panache/

I think it might be possible using a bedgraph -> bigwig conversion, and then individual customized tracks with low track height, eg 50px. But could something more elegant be done ?

For example the below matrix would be represented by 3 separate bedgraphs/bigwigs, each containing the binary presence absence data in the last 3 columns.

Input format tsv input example (more at https://odgi.readthedocs.io/en/latest/rst/tutorials/presence_absence_variants.html )

chr1  10000 20000 1 0 0
chr1  20000 30000 0 1 0

Thanks,
Colin

[cmdcolin]

It would definitely be great to add pangenome "presence absence" (PAV) visualizations

one option would be converting your data format from TSV to VCF so that https://github.com/elsiklab/multivariantviewer could interpret

that way you can keep multi-column

as you mentioned, you could also make a sort of 'binary bedgraph/bigwig' for each sample, and use e.g. multibigwig for that

we also had a user that was looking at PAV and used https://github.com/cmdcolin/jbrowse_piechart

[colindaven]

Great, thanks for those tips. The piechart one is very new for me.

I think I'll try the bedgraph one first, but what do you mean by
use e.g. multibigwig for that

Is there a JBrowse1 multibigwig component, or do you mean for creation of bigwig files ?

• edit - found it - https://github.com/elsiklab/multibigwig