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Generate Synthetic Consortium Metabolism

Source: R/synCM.R
synCM.Rd

Creates a synthetic metabolic network with random species-metabolite interactions and flux values. Useful for testing and demonstrating ramen package functionality.

Usage

synCM(
  name,
  n_species,
  max_met,
  scale_fac = 2,
  seed = FALSE,
  dead_ends = FALSE,
  cm = TRUE
)

Arguments

name

Character string. Name for the consortium.

n_species

Integer. Number of species in the consortium.

max_met

Integer. Size of the metabolite pool to sample from.

scale_fac

Integer. Multiplier for the initial species name pool from which n_species are sampled. Defaults to 2.

seed

Integer or FALSE. Random seed for reproducibility. If FALSE (default), a random seed is chosen.

dead_ends

Logical. If FALSE (default), ensures each species has both consumed and produced metabolites by flipping one flux value when all fluxes share the same sign.

cm

Logical. If TRUE (default), returns a ConsortiumMetabolism object. If FALSE, returns the raw edge list as a tibble.

Value

A ConsortiumMetabolism object when cm = TRUE, or a tibble with columns species, metabolites, and fluxes when cm = FALSE.

Details

Each species is assigned a random subset of metabolites (between 2 and max_met) with normally distributed flux values. By default, species are guaranteed to have both positive and negative fluxes (i.e., no dead ends).

Examples

synCM("Ex. Community", n_species = 5, max_met = 10)
#> 
#> ── ConsortiumMetabolism 
#> Name: "Ex. Community"
#> Weighted metabolic network with 10 metabolites.

# Return raw edge list instead
synCM("Test", n_species = 3, max_met = 8, cm = FALSE)
#> # A tibble: 15 × 3
#>    species  metabolites fluxes
#>    <chr>    <chr>        <dbl>
#>  1 SCE6853Y met3         1.03 
#>  2 SCE6853Y met1        -1.91 
#>  3 PVO1450E met6         5.15 
#>  4 PVO1450E met3         2.32 
#>  5 PVO1450E met7         3.67 
#>  6 PVO1450E met8         0.309
#>  7 PVO1450E met4         2.33 
#>  8 PVO1450E met1         0.338
#>  9 PVO1450E met5        -4.77 
#> 10 ZRK8603K met4        -1.38 
#> 11 ZRK8603K met7         5.40 
#> 12 ZRK8603K met8         4.35 
#> 13 ZRK8603K met6        -0.899
#> 14 ZRK8603K met5        -0.685
#> 15 ZRK8603K met2        -0.965