Extract a Cluster

Extracts a cluster from a ConsortiumMetabolismSet object.

Usage

extractCluster(
  object,
  node_id,
  name = NA_character_,
  description = NA_character_
)

# S4 method for class 'ConsortiumMetabolismSet'
extractCluster(
  object,
  node_id,
  name = NA_character_,
  description = NA_character_
)

Arguments

object

A ConsortiumMetabolismSet object.

node_id

Numeric scalar giving the node to be extracted.

name

Character scalar specifying a name for the selection.

description

Character scalar describing the selection.

Value

A ConsortiumMetabolismSet object containing the extracted cluster.

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 [10ms]
#> 
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [28ms]
#> 
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [25ms]
#> 
#> ℹ Expanding 2 binary matrices to 6-dimensional space
#> ✔ Expanding 2 binary matrices to 6-dimensional space [21ms]
#> 
#> ℹ Computing 6 x 6 levels matrix
#> ✔ Computing 6 x 6 levels matrix [22ms]
#> 
#> 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 "test" created: 2 consortia, 6 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [76ms]
#> 
extractCluster(cms, node_id = 1)
#> 
#> ── Creating CMS "Cluster 1 from 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 [25ms]
#> 
#> 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 [24ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [22ms]
#> 
#> 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 [27ms]
#> 
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [22ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "Cluster 1 from test" created: 2 consortia, 6 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [75ms]
#> 
#> 
#> ── ConsortiumMetabolismSet 
#> Name: "Cluster 1 from test"
#> 2 consortia, 7 species, 6 metabolites.
#> Community size (species): min 3, mean 3.5, max 4.
#> Community size (metabolites): min 2, mean 3.5, max 5.
#> Pathways: 0 pan-cons, 8 niche, 0 core, 6 aux (quantile = 0.1).
#> Species: 1 generalists, 5 specialists (quantile = 0.15).