micom.interaction¶
Submodules¶
Functions¶
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Quantify interactions of a focal/reference taxon with other taxa. |
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Calculate the Metabolic Exchange Score (MES) for each metabolite. |
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Summarize interactions to key quantities. |
Package Contents¶
- micom.interaction.interactions(results: micom.workflows.GrowthResults, taxa: None | str | List[str], threads: int = 1, progress: bool = True) pandas.DataFrame[source]¶
Quantify interactions of a focal/reference taxon with other taxa.
- Parameters:
results (GrowthResults) – The growth results to use.
taxa (str, list of str, or None) – The focal taxa to use. Can be a single taxon, a list of taxa or None in which case all taxa are considered.
- Returns:
The mapped interactions between the focal taxon and all other taxa.
- Return type:
pandas.DataFrame
- micom.interaction.MES(results: micom.workflows.GrowthResults, cutoff: float = None) pandas.DataFrame[source]¶
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
- micom.interaction.summarize_interactions(ints: pandas.DataFrame) pandas.DataFrame[source]¶
Summarize interactions to key quantities.
- Parameters:
ints (pandas.DataFrame) – The interactions for individual metabolites calculated before.
- Returns:
The summarized interactions contaning the total flux, mass flux, carbon flux, nitrogen flux and number of interactions between any pair of taxa in that sample.
- Return type:
pandas.DataFrame