search

ShobiStassen / VIA

trajectory inference
https://pyvia.readthedocs.io/en/latest/
MIT License
78 stars 20 forks source link

About running and extract the result #7

Open tianlt opened 2 years ago

tianlt commented 2 years ago

Hi again,

I followed the jupyter example and found that there are different versions of function to run the VIA; via_wrapper, via.draw_trajectory_gams, or via.VIA etc. I have datasets and want to infer the trajectory using VIA just being doubt about which one suits the most?

Additionally, after running the via_wrapper there are several plots being generated. Is the one named pseudotime the main result that inferred from VIA? And how to save one of diagram(i.e. the pseudotime plot)?

Thank you in advance!

ShobiStassen commented 1 year ago

Hi, If you check out the readthedocs Tutorials which have notebooks and videos, that should help you out. Perhaps a good idea to update to latest version of Via on pip too

Starlitnightly commented 1 year ago

Hi, You can use adata.obs['pt']=v0.single_cell_pt_markov to extract the pseudotime calculated by VIA.