Set of ConsortiumMetabolism Objects

Creates a ConsortiumMetabolismSet combining multiple ConsortiumMetabolism objects into a unified metabolite space. Computes pairwise overlap scores and builds a dendrogram for clustering.

Usage

ConsortiumMetabolismSet(
  ...,
  name = NA_character_,
  desc = NA_character_,
  linkage = "complete",
  verbose = TRUE
)

Arguments

...

Lists or individual ConsortiumMetabolism objects.

name

Character scalar giving the name of the set.

desc

Optional short description of the set.

linkage

Character scalar specifying the agglomeration method for hierarchical clustering of the overlap matrix. Passed to hclust as the method argument. Defaults to "complete", which produces compact clusters where every pair of consortia within a cluster has dissimilarity below the merge threshold.

verbose

Logical scalar. If TRUE (default), prints progress messages during construction.

Value

A ConsortiumMetabolismSet object.

Slots

Name

character. Display name for the set.

Consortia

list. List of ConsortiumMetabolism objects.

Description

character. Optional short description.

OverlapMatrix

matrix. Pairwise dissimilarity matrix (1 - overlap) between consortia.

Dendrogram

list. Hierarchical clustering dendrogram.

NodeData

data.frame. Internal node positions from the dendrogram.

Graphs

list. Named list of igraph objects, one per consortium.

BinaryMatrices

list. Named list of binary matrices expanded to universal metabolite space.

Pathways

data.frame. Combined pathway list from all consortia with re-indexed metabolite positions.

Metabolites

data.frame. Metabolite mapping between per-consortium and universal indices.

See also

ConsortiumMetabolism, TreeSummarizedExperiment-class

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 = "example")
#> 
#> ── Creating CMS "example" ──────────────────────────────────────────────────────
#> ℹ Validating 2 <ConsortiumMetabolism> objects
#> ✔ Validating 2 <ConsortiumMetabolism> objects [12ms]
#> 
#> ℹ Collecting metabolites from 2 consortia
#> ✔ Collecting metabolites from 2 consortia [38ms]
#> 
#> ℹ Re-indexing 7 unique metabolites
#> ✔ Re-indexing 7 unique metabolites [32ms]
#> 
#> ℹ Expanding 2 binary matrices to 7-dimensional space
#> ✔ Expanding 2 binary matrices to 7-dimensional space [22ms]
#> 
#> ℹ Computing 7 x 7 levels matrix
#> ✔ Computing 7 x 7 levels matrix [24ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [24ms]
#> 
#> 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 [21ms]
#> 
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [23ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "example" created: 2 consortia, 7 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [82ms]
#> 
cms
#> 
#> ── ConsortiumMetabolismSet 
#> Name: "example"
#> 2 consortia, 7 species, 7 metabolites.
#> Community size (species): min 3, mean 3.5, max 4.
#> Community size (metabolites): min 2, mean 4, max 6.
#> Pathways: 0 pan-cons, 19 niche, 0 core, 14 aux (quantile = 0.1).
#> Species: 2 generalists, 3 specialists (quantile = 0.15).