Get Functional Groups

Calculates and returns functional groups based on metabolic reactions. For ConsortiumMetabolismSet objects, this involves analyzing shared reactions across species to identify clusters of species with similar metabolic capabilities.

Usage

functionalGroups(object, k = 4, ...)

# S4 method for class 'ConsortiumMetabolismSet'
functionalGroups(object, k = 4, label_size = 6, label_colours = NULL)

Arguments

object

A ConsortiumMetabolismSet object.

k

An integer scalar specifying the number of clusters to color in the dendrogram.

...

Additional arguments to be passed to specific methods.

label_size

Numeric scalar specifying label size in the output plot.

label_colours

If not NULL, a tibble with columns label and colour.

Value

A list (returned invisibly) containing:

• plot: The ggplot2 dendrogram visualization

• dendrogram: The dendrogram object

• similarity_matrix: Matrix of Jaccard similarities between species

• species_combinations: Tibble with pairwise species comparisons

• reactions_per_species: Tibble mapping species to their reactions

The plot is automatically displayed.

Details

This method is currently implemented for ConsortiumMetabolismSet objects. Future versions will extend functionality to ConsortiumMetabolismAlignment objects to allow for comparative functional group analysis across different alignments.

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 [30ms]
#> 
#> 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 [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 [22ms]
#> 
#> ℹ Extracting dendrogram node positions
#> ✔ Extracting dendrogram node positions [24ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> ✔ CMS "test" created: 2 consortia, 6 metabolites (0.2s)
#> ℹ Collecting 2 consortium graphs

#> ✔ Collecting 2 consortium graphs [81ms]
#> 
functionalGroups(cms, k = 2)
#> Loading required namespace: colorspace
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the dendextend package.
#>   Please report the issue at <https://github.com/talgalili/dendextend/issues>.

# }