RNA velocity and fig3 in the Genome Bio paper

[DHGK]

Hi PAGA community,

In the PAGA genome bio paper fig3 c,d, it shows how users could integrate RNA velocity information with PAGA to generated a directed PAGA graph. I really think that this is an amazing feature and wish to try out!

However, when going through fig3 example notebook, I feel the example stops right after fig3 b without showing vignettes for c,d. I'm wondering if anyone has tried to incorporate RNA velocity info and would like to share how you did it?

Thanks!

[falexwolf]

Getting the figure based on velocyto involved quite a bit of book keeping of objects etc.

These days, if you use @VolkerBergen's scvelo, it should be much easier to get results like this. @VolkerBergen adapted the code to match his package: Do you have an example that we could link to also from here, so that people can find it? The Dentate Gyrus, for instance?

[VolkerBergen]

@DHGK you can follow this example to obtain velocities, and compute directed PAGA via

scv.tl.velocity_graph(adata)

sc.tl.paga(adata)
sc.tl.paga(adata, use_rna_velocity=True)

sc.pl.paga(adata, transitions='transitions_confidence')

[DHGK]

@falexwolf and @VolkerBergen ,

Thank you so much for your suggestions. I'll try out the scvelo package to see what I get.

[VolkerBergen]

An example of applying directed PAGA can be found at https://scvelo.readthedocs.io/VelocityBasics.html.