theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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The result is contrary to the expectation, is there a better suggestion? #1139

Closed Jingle0814 closed 9 months ago

Jingle0814 commented 10 months ago

Hi, ...When I use the ”Stochastic“ and ”dynamical“ models, the results are not consistent with my expectations, because my cell type has a clear differentiation trajectory, is there any better parameter suggestions?

# paste your code here, if applicable
```data2_sub=sc.read("../../input/Files/Velocity/data2_sub_new.h5ad")
scv.pp.filter_and_normalize(data2_sub)
scv.pp.moments(data2_sub)

### dynamical
scv.tl.recover_dynamics(data2_sub,n_jobs=60)
scv.tl.velocity(data2_sub, mode='dynamical',n_jobs=60)
scv.tl.velocity_graph(data2_sub,n_jobs=60)

### stochastic
scv.tl.velocity(data2_sub, mode='stochastic',n_jobs=60)
scv.tl.velocity_graph(data2_sub,n_jobs=60)

<!-- Error Output -->
<details>
The two outputs were different and neither was consistent with my expectations

<summary> Error output </summary>

```pytb
# paste the error output here, if applicable

Versions ```pytb # paste the ouput of scv.logging.print_versions() here ```scvelo==0.2.5 scanpy==1.9.2 anndata==0.8.0 loompy==3.0.7 numpy==1.22.4 scipy==1.9.1 matplotlib==3.6.2 sklearn==1.2.1 pandas==1.5.1