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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Graph connectivities metric #328

Closed Chengwei94 closed 2 years ago

Chengwei94 commented 2 years ago

Hi there,

shouldnt graph connectivity use adata.obsp["distances"] or some sort of shared nearest neighbors as the graph, since that adata.obsp["connectivities"] might connect distant nodes together to ensure that the whole graph is connected and lead to spurious edges?

LuckyMD commented 2 years ago

Hi @Chengwei94,

If you check the connectivities matrix you will see that only the nearest neighbours of any node have a non-zero connectivity (the same nodes that also have a reported distance). Thus, the whole graph will not necessarily be connected when using connectivities. Connetivities are a function of distance (I would have to look up exactly what that function is) that is scaled between 0 and 1 and is inversely related to distance. Thus, it is more fitting than distances here.