pyucell.compute_scores_from_ranks

pyucell.compute_scores_from_ranks#

pyucell.compute_scores_from_ranks(adata, ranks, signatures, max_rank=1500, missing_genes='impute', w_neg=1.0, suffix='_UCell')#

Compute UCell scores from a pre-computed rank matrix.

Use this when scoring multiple signature sets against the same dataset: compute ranks once with get_rankings, then call this function for each set of signatures without re-ranking.

Parameters:

  • adata (AnnData) – AnnData object whose obs will receive the scores. Must share var_names and obs_names with the object used to compute ranks.

  • ranks (csr_matrix of shape (n_genes, n_cells)) – Pre-computed rank matrix from get_rankings.

  • signatures (dict[str, list[str]]) – Signature name → list of gene names.

  • max_rank (int) – Must match the max_rank used in get_rankings.

  • missing_genes (str) – “impute”: missing genes are treated as max_rank. “skip”: missing genes are excluded.

  • w_neg (float) – Weight on negative gene sets.

  • suffix (str) – Appended to each signature name when writing to adata.obs.

Return type:

None