generate_combined_graphs function

Combines individual layers to a single graph

Individual graphs created by generate_individual_graphs

are combined to a single graph per group according to inter_layer_connections. Returns a list of combined graphs along with their annotations.

generate_combined_graphs(
  graphs,
  annotations,
  inter_layer_connections,
  settings
)

Arguments

• graphs: [list] A named list (elements groupA and groupB). Each element contains a list of iGraph objects (graphs from output of generate_individual_graphs).
• annotations: [list] A named list (elements groupA, groupB and both). Each element contains a list of data frames mapping each node IDs to identifiers. both contains unique identifiers across the whole data. (annotations from output of generate_individual_graphs)
• inter_layer_connections: [list] Named list with specified inter-layer connections. Names are layer names and elements are connections (make_connection ).
• settings: [list] A named list containing pipeline settings. The settings list has to be initialized by drdimont_settings. Items in the named list can be adjusted as desired.

Returns

A named list (elements graphs and sub-elements $groupA and $groupB, and annotations and sub-element both). Contains the igraph objects of the combined network and their annotations for both groups.

Examples

data(individual_graphs_example)
data(metabolite_protein_interactions)

example_inter_layer_connections = list(make_connection(from='mrna', to='protein',
                                           connect_on='gene_name', weight=1),
                                       make_connection(from='protein', to='phosphosite',
                                           connect_on='gene_name', weight=1),
                                       make_connection(from='protein', to='metabolite',
                                           connect_on=metabolite_protein_interactions,
                                           weight='combined_score'))

example_settings <- drdimont_settings()

example_combined_graphs <- generate_combined_graphs(
                               graphs=individual_graphs_example$graphs,
                               annotations=individual_graphs_example$annotations,
                               inter_layer_connections=example_inter_layer_connections,
                               settings=example_settings)