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

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

# S4 method for class 'ConsortiumMetabolismSet'
getFunctionalGroups(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, tb with two columns, label and colour.

Value

A dendrogram object representing the hierarchical clustering of species into functional groups. The plot of the dendrogram is also 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.