omicverse.micro.paired_spearman

omicverse.micro.paired_spearman#

omicverse.micro.paired_spearman(adata_microbe, adata_metabolite, clr_microbe=True, log1p_metabolite=True, min_prevalence=0.0)[source]#

Rank correlation between every (microbe, metabolite) pair.

Parameters:

  • adata_microbe (AnnData) – Must share obs_names (same samples, same order).

  • adata_metabolite (AnnData) – Must share obs_names (same samples, same order).

  • clr_microbe (bool (default: True)) – CLR-transform the microbes first (recommended — compositional data).

  • log1p_metabolite (bool (default: True)) – log(1 + x)-transform the metabolites first.

  • min_prevalence (float (default: 0.0)) – Drop microbes present in < this fraction of samples before testing (Spearman is undefined on constant rows).

Return type:

DataFrame

Returns:

  • DataFrame with columns microbe / metabolite / rho / p_value / fdr_bh

  • sorted by p_value ascending.

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