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labgem / PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes
https://ppanggolin.readthedocs.io
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User-Defined Filtering and Annotation #78

Closed seajane closed 1 year ago

seajane commented 2 years ago

Hello!

I am not sure if I have missed something in the wiki or this is possible in some way I haven't quite figured out, so I am reaching out to see if you can point me in the correct direction. I have a pangenome graph that I am viewing in Gephi that I would love to be able to take a defined subset of ORF from the underlying collection (e.g. found enriched in a specific niche) and ask the question "which nodes on the pangenome image do these ORF fall into, and are those nodes forming syntenic blocks across the pangenome?" Further, it would be incredibly advantageous to be able to do this en-masse with collections of genes (user-defined subsets of ORF) and create something like a 'user defined' partition (that can be handled in the same way as ppanggolin-defined partitions (highlight all on Gephi image, color change, etc.).

Thanks!

jpjarnoux commented 2 years ago

Hi, I never try, but maybe is possible. I will search information and come back to you ASAP. Thanks

ggautreau commented 2 years ago

Hi @seajane,

Using Gephi, you can filter the nodes based on a particular query https://www.youtube.com/watch?v=0R86bJVxMrA

So you can filter gene families belonging to some specific genomes. Just make sure to use the full gexf file pangenomeGraph.gexf with the genome information and not the lighter one. You can then filter persistent families to visualize variable synteny blocs (from shell and cloud families).

But indeed, RGP, spots and panModules are not exported in the GEXF file, it could be an enhancement to add them in this output file in order to improve the exploration of the graph.

Moreover, we are working on an ad hoc visualization interface dedicated to the exploration of pangenome graph but it is a huge work, still in progress.

Best regards.

seajane commented 2 years ago

@ggautreau Thank you so much for looking into this and I appreciate the link to the Gephi tutorial. This link is great for showing the filtering feature after the partition is populated. What I am looking to find is a way to populate the partition with different data.

I look forward to seeing the new updates, they sound very exciting!

Best of Luck!