visionpy.compute_signatures_anndata#

visionpy.compute_signatures_anndata(adata, norm_data_key, signature_varm_key, signature_names_uns_key)[source]#

Compute signatures for each cell.

Parameters:

  • adata (AnnData) – AnnData object to compute signatures for.

  • norm_data_key (Union[Literal['use_raw'], str]) – Key for adata.layers to use for signature computation. If “use_raw”, use adata.raw.X.

  • signature_varm_key (str) – Key in adata.varm for signatures. If None (default), no signatures. Matrix should encode positive genes with 1, negative genes with -1, and all other genes with 0

  • signature_names_uns_key (str) – Key in adata.uns for signature names. If None, attempts to read columns if signature_varm_key is a pandas DataFrame. Otherwise, uses Signature_1, Signature_2, etc.

Return type:

None