Plot Functional Groups Dendrogram

Visualizes the functional groups dendrogram computed by functionalGroups. Branches are colored by cluster membership and species labels are placed below the dendrogram.

Usage

plotFunctionalGroups(fg, k = 4, label_size = 3, label_colours = NULL)

Arguments

fg

A list as returned by functionalGroups, containing at least a dendrogram element.

k

Integer scalar specifying the number of clusters to color in the dendrogram. Default 4.

label_size

Numeric scalar specifying the text size for species labels. Default 3.

label_colours

If not NULL, a data frame with columns label and colour mapping species names to colors. When NULL (default), all labels are drawn in black.

Value

A ggplot object.

See also

functionalGroups for computing the functional groups data.

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 [11ms]
#> 
#> 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 [23ms]
#> 
#> 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 [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 [24ms]
#> 
#> ℹ Collecting 2 consortium graphs
#> CMS "test" created: 2 consortia, 7 metabolites (0.2s)
#> ✔ Collecting 2 consortium graphs [93ms]
#> 
fg <- functionalGroups(cms)
plotFunctionalGroups(fg, k = 2)