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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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Shape of phase plot(U-S) changes after scv.pp.moments(adata) #1253

Closed yuzzini closed 1 month ago

yuzzini commented 1 month ago

Hi, thank you for developing this tool. I have a question about the shape of a phase plot

Before calculating scv.pp.moments, scv.pp.normalize_per_cell(adata) scv.pl.scatter(adata, basis=['FTL'])

results in image

and this is consistent which I checked through my own code doing total count normalization image

but, after doing scv.pp.moments(adata)

phase plot dramatically change, like below, image

why is this happening? and which is a correct phase plot?

Sorry if this is a question lacking an understanding of scVelo's essense, but I would appreciate it if you could explain why this is happening.

Thank you,

WeilerP commented 1 month ago

Please check the docs for these sort of questions. If moments exist, scatter plots them by default.