Retrieve all modules a physical node is assigned to in python API

[u-xixi]

Hi

Sorry if i'm spamming you again. I'm using the python API to partition a multilayer network. And I want to get all the modules each physical node is assigned to, using the Infomap object. I know I can write out a .clu file and parse that, but it seems like a detour.

I know that I can call get_modules(states=False) to retrieve node_id: module_id assignment. But in this case, if the physical node has states in multiple modules, I can get only one of them. get_modules(states=False) instead has state_id as the key. But I didn't find out how to bridge the state_id and their physical node_id directly.

Maybe a bit more context: I study bioinformatics and the nodes are genome fragments. I'm exploring if the overlapping clustering could even perform better than the traditionally non-overlapping way. My network was created layer by layer, in each layer, link by link, using add_multilayer_intra_link(). The state nodes are made internally by Infomap, so I would not know what states each physical node has.

thanks in advance,
Xixi

[danieledler]

Hi @u-xixi,

For a multilayer network, you can access the node_id and layer_id together with module_id when you iterate the (state) nodes:

for node in im.nodes:
    print(node.node_id, node.layer_id, node.module_id)

This will give you overlapping modules, as the same node_id may occur multiple times for different layer_id.

See this example.