generate_combined_graphs {DrDimont} | R Documentation |
Combines individual layers to a single graph
Description
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.
Usage
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 |
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 |
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 |
Value
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)