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MiCo (Microbial Community) Class

class-MiCo.Rmd

MiCo

The MiCo class serves as the standard way to save and work with data on the metabolism, the function, of a microbial community.

Creation from data

To create an object of type MiCo, the user must input the data listed below. This data can either be contained in a single tibble or data frame, saved in a CSV file, or input as separate vectors.

  • species: A character vector specifying the species present in the community.
  • metabolites: A character vector specifying the metabolites present in the community.
  • fluxes: A numeric vector specifying the fluxes of each metabolite in the community.
  • name: Character string giving the name of the community.
s <- c("RQR9693L", "RQR9693L", "RQR9693L", "RQR9693L", "MEV1152G", "MEV1152G", "MEV1152G", "XIQ2234Q", "XIQ2234Q", "XIQ2234Q")
m <- c("met3", "met1", "met4", "met4", "met3", "met2", "met2", "met3", "met4", "met1")
f <- c(-0.3023640,  0.5344641, -2.2337716, 3.3063823, 2.5520278, 0.3388498, -1.8460633, -1.3043675, -0.4788769,  0.6027292)

newMiCo(species = s, metabolites = m, fluxes = f, name = "example_MiCo")
#> example_MiCo: MiCo (MicrobialCommunity) Object
#> - Unique microorganisms (MO): 3
#> - Unique metabolites (met): 4

fsmc provides the function syn_community() to generate random MiCo objects based on user parameters.

makeSynMiCo(n_species = 8, max_met = 10, name = "example_syn_MiCo")
#> example_syn_MiCo: MiCo (MicrobialCommunity) Object
#> - Unique microorganisms (MO): 8
#> - Unique metabolites (met): 10

Create a MiCo Object from a tibble

fsmc contains a set of example data that can be used for the analysis of microbial communities. For this example, we will use data created by MiSoS(oup). Two example communities are provided in the package ac_A1R12_1 and cit_A1R12_1.

The MiCo function can take either a path to a .csv file or a data frame/tibble as input.

Contents

Upon the creation of a MiCo class based on a three column input, additional information is calculated:

  • species
  • metabolites
  • fluxes
  • edges
  • binary matrix
  • flux matrix
  • name
  • flux_consumption
  • flux_production
  • effective_flux_consumption
  • effective_flux_production

Each of these slots is described in the MiCo-class() class documentation.

Methods

  • getCo(): Returns the community in tibble format.
  • getSpecies(): Retrieves the species from a community.
  • getMet(): Retrieves metabolites from a community.
  • getFlux(): Retrieves the fluxes from a community.
  • getEdges(): Retrieves the edges from a community.