Functional Microbiome Representation based on TreeSummarizedExperiment

Functional Microbiome Representation based on TreeSummarizedExperiment

Usage

MicrobiomeFunction(
  data,
  name = NA_character_,
  species_col = "species",
  metabolite_col = "met",
  flux_col = "flux",
  ...
)

data: a DataFrame-like object that includes columns specfiying the species, metabolites and fluxes in the microbiome. The fluxes can either be weighted or unweighted (all of magnitude 1).
name: a character scalar specifying the name of the Microbiome
species_col: Character scalar specfiying the name of the species column, defaults to 'spec'.
metabolite_col: Character scalar specifying the name of the metabolite column, defaults to 'met'.
flux_col: Character scalar specifying the name of the flux column, defaults to 'flux'.
...: Additional arguments to be passed to the constructor.