omicverse.single.format_liana_results

omicverse.single.format_liana_results#

omicverse.single.format_liana_results(adata=None, *, liana_res=None, uns_key='liana_res', score_key='specificity_rank', pvalue_key='specificity_rank', inverse_score=True, inverse_pvalue=False, classification=None, classification_reference='cellchat', classification_fallback='family')[source]#

Format LIANA results into the communication AnnData expected by ov.pl.ccc_*.

Parameters:

  • adata (default: None) – AnnData containing adata.uns[uns_key].

  • liana_res (DataFrame | None (default: None)) – LIANA result table. If omitted, it is read from adata.uns[uns_key].

  • uns_key (str (default: 'liana_res')) – Key in adata.uns that stores the LIANA result DataFrame.

  • score_key (str (default: 'specificity_rank')) – Column used to populate layers['means']. For current aggregated LIANA results, 'specificity_rank' is the safest default because 'magnitude_rank' can be empty on some datasets.

  • pvalue_key (str (default: 'specificity_rank')) – Column used to populate layers['pvalues']. For aggregated LIANA results, 'specificity_rank' is recommended.

  • inverse_score (bool (default: True)) – Whether smaller values in score_key should be transformed to larger communication strengths. This should stay True for rank-based scores.

  • inverse_pvalue (bool (default: False)) – Whether smaller values in pvalue_key should be inverted before being written to layers['pvalues']. Keep False for rank / p-value-like columns where smaller values indicate stronger support.

  • classification (Union[str, Mapping[str, str], None] (default: None)) – Optional column name or ligand-receptor mapping used to populate var['classification'].

  • classification_reference (str | DataFrame | None (default: 'cellchat')) – Optional built-in reference ('cellchat', 'cellchat_human', 'cellchat_mouse') or a custom DataFrame used to backfill pathway annotations for interactions not covered by classification.

  • classification_fallback (str | None (default: 'family')) – Fallback strategy for interactions still not covered after reference matching. Use 'family' for coarse signaling-family hints, a custom string for a fixed fallback label, or None to keep 'Unclassified'.

Returns:

Communication AnnData with obs cell-type pairs and var LR pairs.

Return type:

anndata.AnnData

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