Plot a ConsortiumMetabolismSet object

Usage

# S4 method for class 'ConsortiumMetabolismSet,ANY'
plot(x, label_colours = NULL, max_nodes = 20, label_size = 4)

Arguments

x: A ConsortiumMetabolismSet object.
label_colours: Optional tibble with label and colour columns.
max_nodes: Maximum number of dendrogram nodes.
label_size: Numeric label size.

Value

A ggplot object (returned invisibly).

Examples

# \donttest{
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 [31ms]
#> 
#> ℹ Re-indexing 6 unique metabolites
#> ✔ Re-indexing 6 unique metabolites [28ms]
#> 
#> 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 [24ms]
#> 
#> ℹ Computing pairwise overlap (1 pairs via crossprod)
#> ✔ Computing pairwise overlap (1 pairs via crossprod) [23ms]
#> 
#> ℹ Assembling pathway data from 2 consortia
#> ✔ Assembling pathway data from 2 consortia [30ms]
#> 
#> 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, 6 metabolites (0.2s)
#> ℹ Collecting 2 consortium graphs

#> ✔ Collecting 2 consortium graphs [79ms]
#> 
plot(cms)

# }