Returns the pairwise dissimilarity matrix from a
ConsortiumMetabolismSet object. Values are
1 - FOS (Functional Overlap Score), so 0
indicates identical consortia and 1 indicates no
shared pathways.
Value
A numeric \(n \times n\) matrix of pairwise dissimilarities, where \(n\) is the number of consortia. Row and column names are consortium names.
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 [30ms]
#>
#> ℹ Re-indexing 7 unique metabolites
#> ✔ Re-indexing 7 unique metabolites [26ms]
#>
#> 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) [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 [21ms]
#>
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [31ms]
#>
#> ℹ Collecting 2 consortium graphs
#> CMS "test" created: 2 consortia, 7 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [74ms]
#>
overlapMatrix(cms)
#> comm_1 comm_2
#> comm_1 0.0 0.8
#> comm_2 0.8 0.0