Show Method for ConsortiumMetabolismSet Object

Show Method for ConsortiumMetabolismSet Object

Usage

# S4 method for class 'ConsortiumMetabolismSet'
show(object)

Arguments

object

An object of class ConsortiumMetabolismSet

Value

The object, invisibly.

Examples

cm1 <- synCM("comm_1", n_species = 3, max_met = 5)
cm2 <- synCM("comm_2", n_species = 4, max_met = 6)
cms <- ConsortiumMetabolismSet(cm1, cm2, name = "test")
#> 
#> ── Creating CMS "test" ─────────────────────────────────────────────────────────
#> ℹ Validating 2 <ConsortiumMetabolism> objects
#> ✔ Validating 2 <ConsortiumMetabolism> objects [11ms]
#> 
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [29ms]
#> 
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [26ms]
#> 
#> ℹ Expanding 2 binary matrices to 6-dimensional space
#> ✔ Expanding 2 binary matrices to 6-dimensional space [23ms]
#> 
#> ℹ Computing 6 x 6 levels matrix
#> ✔ Computing 6 x 6 levels matrix [33ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [25ms]
#> 
#> ℹ Assembling pathway data from 2 consortia
#> ✔ Assembling pathway data from 2 consortia [29ms]
#> 
#> 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 [23ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "test" created: 2 consortia, 6 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [76ms]
#> 
show(cms)
#> 
#> ── ConsortiumMetabolismSet 
#> Name: "test"
#> 2 consortia, 7 species, 6 metabolites.
#> Community size (species): min 3, mean 3.5, max 4.
#> Community size (metabolites): min 4, mean 5, max 6.
#> Pathways: 2 pan-cons, 18 niche, 0 core, 16 aux (quantile = 0.1).
#> Species: 2 generalists, 2 specialists (quantile = 0.15).