running on selected cells

[aminzia]

Hello everyone,

I was wondering if there's a way to run scvelo on a selected set of 10X gex cells (a subset of barcodes).

Thank you all in advance.
Amin

[WeilerP]

Currently, there is no such option in scvelo. I guess you were hoping for some keyword argument like var_names in scv.tl.recover_dynamics. The reason this is not as easily possible is that subsetting observations requires also recalculating the neighbor graph and subsequently imputation and latent space embedding.
To summarise: To run scvelo on a subset of your observations, you will have to subset the data manually:

adata_subsetted = adata[obs_subset, :]

# preprocessing
scv.pp.moments(adata_subsetted)

# inference
scv.tl.recover_dynamics(adata_subsetted)