Coerce a ConsortiumMetabolismSet to a data.frame

Row-binds the per-consortium edge lists of every ConsortiumMetabolism in the set, prefixing each row with a consortium column.

Usage

# S4 method for class 'ConsortiumMetabolismSet'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x

A ConsortiumMetabolismSet object.

row.names

Ignored.

optional

Ignored.

...

Additional arguments (currently unused).

Value

A data.frame with columns consortium, met, species, and flux. Empty sets return a 0-row data.frame with the same column names.

Examples

cm1 <- synCM("a", n_species = 3, max_met = 5)
cm2 <- synCM("b", n_species = 3, max_met = 5)
cms <- ConsortiumMetabolismSet(list(cm1, cm2), name = "demo")
#> 
#> ── Creating CMS "demo" ─────────────────────────────────────────────────────────
#> ℹ Validating 2 <ConsortiumMetabolism> objects
#> ✔ Validating 2 <ConsortiumMetabolism> objects [10ms]
#> 
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [28ms]
#> 
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [24ms]
#> 
#> ℹ Expanding 2 binary matrices to 6-dimensional space
#> ✔ Expanding 2 binary matrices to 6-dimensional space [22ms]
#> 
#> ℹ Computing 6 x 6 levels matrix
#> ✔ Computing 6 x 6 levels matrix [23ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [21ms]
#> 
#> ℹ Assembling pathway data from 2 consortia
#> ✔ Assembling pathway data from 2 consortia [28ms]
#> 
#> ℹ Building dendrogram from 2 x 2 dissimilarity matrix
#> ✔ Building dendrogram from 2 x 2 dissimilarity matrix [20ms]
#> 
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [22ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "demo" created: 2 consortia, 6 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [81ms]
#> 
head(as.data.frame(cms))
#>   consortium  met  species       flux
#> 1          a met2 QWG2904R -2.3108858
#> 2          a met2  GRW821Q -1.8850686
#> 3          a met5  GRW821Q  8.7532211
#> 4          a met5 GIH4406S -2.7387147
#> 5          a met2 GIH4406S  4.1959544
#> 6          a met3 QWG2904R  0.4356225