Network Generators¶
magine.networks.network_generator module¶
- magine.networks.network_generator.build_network(seed_species, species='hsa', save_name=None, all_measured_list=None, trim_source_sink=False, use_reactome=True, use_hmdb=False, use_biogrid=True, use_signor=True, verbose=False)[source]¶
Construct a network from a list of gene names.
- Parameters
- seed_specieslist
list of genes to construct network
- save_namestr, optional
output name to save network. Will save one before and after ID conversion
- speciesstr
species of proteins (‘hsa’: human, ‘mmu’:murine)
- all_measured_listlist
list of all species that should be considered in network
- use_reactomebool
Add ReactomeFunctionalInteraction reaction to network
- use_biogridbool
Add BioGrid reaction to network
- use_hmdbbool
Add HMDB reaction to network all_measured_list
- use_signorbool
Add SIGNOR reaction to network
- trim_source_sinkbool, optional
Remove source and sink nodes if they are not measured in network
- verbosebool
- Returns
- networkx.DiGraph
- magine.networks.network_generator.create_background_network(save_name='background_network', fresh_download=False, verbose=True, create_overlap=False)[source]¶
- Parameters
- save_namestr
Name of the network
- fresh_downloadbool
Download a fresh copy of the databases
- verbose: bool
Print information about the databases
- create_overlapbool
Creates a figure comparing the databses
- Returns
- ——-
- nx.DiGraph
magine.networks.annotated_set module¶
magine.networks.subgraphs module¶
Subpackages¶
The following subpackages to download and parse data