Parent Issue: Functions for investigating networks

asizemore commented 8 months ago

We should do this sooner than expected, because it's a dependency for the Microbiome Paper.

[ ] https://github.com/VEuPathDB/plot.data/issues/239
[ ] make a function to get a node's neighbors
[ ] implement community detection algorithm. Consider (weighted) stochastic block model (ex) or possibly igraph_community_leiden. tbd.
[ ] Some global property like core-periphery ness or small worldness (weighted version).
[ ] Topological overlap

Should have some local (based around a node and its direct neighbors), some mesoscale, and a few global (though that's probably less important in this context).

d-callan commented 8 months ago

today i learned what 'topological overlap' is, and think support for that goes on this list.

d-callan commented 8 months ago

also, can we maybe get more detail and possibly some links for things like small worldness and mesoscale. im still acquiring vocabulary here....

asizemore commented 8 months ago

Good call. Updated the description!

asizemore commented 8 months ago

here's another community detection algorithm worth checking out https://iopscience.iop.org/article/10.1088/1367-2630/16/9/093001

asizemore commented 8 months ago

also seems like a good time https://www.researchgate.net/figure/Unipartite-versus-bipartite-representations-A-Unipartite-graph-of-a-network-comprised_fig5_277620255

VEuPathDB / plot.data

Parent Issue: Functions for investigating networks #242