opened
DHGK
username_0
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!
RNA velocity and fig3 in the Genome Bio paper
issue
created
falexwolf
username_1
Getting the figure based on velocyto involved quite a bit of book keeping of objects etc.

These days, if you use @username_2's `scvelo`, it should be much easier to get results like this. @username_2 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?
comment
created
VolkerBergen
username_2
@username_0 you can follow this [example](https://scvelo-notebooks.readthedocs.io/en/latest/DentateGyrus.html) 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')
```
comment
created
DHGK
username_0
@username_1 and @username_2 ,

Thank you so much for your suggestions. I'll try out the scvelo package to see what I get.
comment
created
VolkerBergen
username_2
An example of applying directed PAGA can be found at https://scvelo.readthedocs.io/VelocityBasics.html.
comment