harreman.tools.compute_interaction_module_correlation

harreman.tools.compute_interaction_module_correlation(adata, cor_method='pearson', test=None, interaction_type='metabolite', only_sig_values=False, normalize_values=False, use_FDR=True, use_super_modules=False)

Compute correlations between interacting cell scores and module scores.

Parameters:

• adata (AnnData) – Must contain: - uns['interacting_cell_results'] (parametric or non-parametric interacting cell scores) - obsm['module_scores'] or obsm['super_module_scores'] - uns['metabolites'] or uns['gene_pairs_sig_names']

• cor_method ({"pearson", "spearman"}, default "pearson") – Statistical method used to compute correlations.

• test ({"parametric", "non-parametric"}) – Which interacting-cell score set to use. - “parametric” → uses uns['interacting_cell_results']['p'] - “non-parametric” → uses uns['interacting_cell_results']['np']

• interaction_type ({"metabolite", "gene_pair"}, default "metabolite") – Select whether to correlate: - metabolite scores, or - gene pair scores.

• only_sig_values (bool, default False) – If True, use only significant interacting cell score values (cs_sig_pval or cs_sig_FDR).

• normalize_values (bool, default False) – Apply min–max normalization to interacting cell score values per interaction.

• use_FDR (bool, default True) – If only_sig_values=True, determines whether to filter by FDR or raw p-values.

• use_super_modules (bool, default False) – Whether to use super-module scores (obsm['super_module_scores']) instead of module scores.