omicverse.utils.cal_paga

omicverse.utils.cal_paga(adata, groups=None, vkey='velocity', use_time_prior=True, root_key=None, end_key=None, threshold_root_end_prior=None, minimum_spanning_tree=True, copy=False)[source]

Compute a PAGA graph with optional velocity/time priors.

Parameters:

  • adata (anndata.AnnData) – Annotated data matrix with neighborhood graph.

  • groups (str or None) – Grouping key in adata.obs; auto-detected when None.

  • vkey (str) – Velocity layer key used for transition confidence.

  • use_time_prior (str or bool) – Pseudotime prior key (or True to auto-use velocity pseudotime).

  • root_key (str or None) – Obs key marking root states.

  • end_key (str or None) – Obs key marking terminal states.

  • threshold_root_end_prior (float or None) – Threshold for root/end priors in [0, 1].

  • minimum_spanning_tree (bool) – Whether to prune graph to most confident tree-like structure.

  • copy (bool) – Whether to return a copied AnnData with computed results.

Returns:

Copied AnnData if copy=True; otherwise results are written in place.

Return type:

anndata.AnnData or None