micom.interaction.focal

Quantify metabolic interactions between taxa.

Module Contents

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.

micom.interaction.focal._metabolite_interaction(fluxes: pandas.DataFrame, taxon: str, partner: str) → pandas.DataFrame

Checks if and how taxa interact.

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

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

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

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