Functions to Change the orientation of MiCo Input Data

Wrapper function around tidyr's pivot_longer() function to facilitate the easy transformation into the correct data format for MiCo construction.

Usage

pivotMiCo(tb, species, from, to, flux)

Arguments

tb: Tibble with data on a microbial community in long or short format to be
species: Column name of the species column
from: the name of the column specifying the met consumed
to: the name of the column specifying the met excreted
flux: Column name of the flux column

Examples

tb <- tibble::tribble(
  ~uptake, ~secretion, ~flux, ~species,
  "m1", "m2", 1, "s1",
  "m2", "m3", 1, "s2",
  "m3", "m4", 1, "s3",
  "m4", "m1", 1, "s4")

pivotMiCo(
    tb = tb,
    species = "species",
    from = "uptake",
    to = "secretion",
    flux = "flux")
#> # A tibble: 8 × 3
#>   species metabolite  flux
#>   <chr>   <chr>      <dbl>
#> 1 s1      m1            -1
#> 2 s1      m2             1
#> 3 s2      m2            -1
#> 4 s2      m3             1
#> 5 s3      m3            -1
#> 6 s3      m4             1
#> 7 s4      m4            -1
#> 8 s4      m1             1