How to impute all genes from SC data for Spatial data

[wjwei-handsome]

Thank you for developing scENVI — it’s a great tool!

As the title says, it seems that scENVI only imputes highly variable genes (default: 2048) in the single-cell data, along with the genes already present in the spatial data. I wonder if it’s possible to impute all genes?

Best regards,
Wenjie

[seanlzheng]

You can just set the num_HVG to the total number of genes in your single cell reference dataset:

N_GENES = sc_adata.n_vars
envi_model = scenvi.ENVI(spatial_data = st_adata, sc_data = sc_adata, num_HVG = N_GENES)