micom.interaction.scores

Various interaction scores.

Functions

_mes(→ float)	Helper to calculate the MES score.
MES(→ pandas.DataFrame)	Calculate the Metabolic Exchange Score (MES) for each metabolite.

Module Contents

micom.interaction.scores._mes(df: pandas.DataFrame) → float

Helper to calculate the MES score.

micom.interaction.scores.MES(results: micom.workflows.GrowthResults, cutoff: float = None) → pandas.DataFrame

Calculate the Metabolic Exchange Score (MES) for each metabolite.

MES is the harmonic mean of producers and consumers for a chosen metabolite in one sample. High values indicate a large prevalence of cross-feeding for the particular metabolite. A value of zero indicates an absence of cross-feeding for the particular metabolite.

Parameters:

• results (GrowthResults) – The growth results to use.

• cutoff (float) – The smallest flux to consider in the analysis. Will default to the solver tolerance if set to None.

Returns:

The scores for each metabolite and each sample including metabolite annotations.

Return type:

pandas.DataFrame

References

[1]

Marcelino, V.R., et al. Disease-specific loss of microbial cross-feeding interactions in the human gut Nat Commun 14, 6546 (2023). https://doi.org/10.1038/s41467-023-42112-w