micom.interaction.focal¶

Quantify metabolic interactions between taxa.

Functions¶

`_metabolite_interaction`(→ pandas.DataFrame)	Checks if and how taxa interact.
`sample_interactions`(→ pandas.DataFrame)	Quantify interactions in a single sammple.
`_interact`(→ pandas.DataFrame)	Quantify interactions of a focal taxon with other taxa.
`interactions`(→ pandas.DataFrame)	Quantify interactions of a focal/reference taxon with other taxa.

Module Contents¶

micom.interaction.focal._metabolite_interaction(fluxes: pandas.DataFrame, taxon: str, partner: str) → pandas.DataFrame[source]¶: Checks if and how taxa interact.

micom.interaction.focal.sample_interactions(fluxes: pandas.DataFrame, sample_id: str, taxon: str) → pandas.DataFrame[source]¶

Quantify interactions in a single sammple.

Parameters:

fluxes (pandas.DataFrame) – A table of exchange fluxes.
sample_id (str) – The sample id to use.
taxon (str) – The focal taxon to use.

Returns:

The mapped interactions between the focal taxon and all other taxa.

Return type:

pandas.DataFrame

micom.interaction.focal._interact(args: List) → pandas.DataFrame[source]¶: Quantify interactions of a focal taxon with other taxa.

micom.interaction.focal.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