feat: add jaccard as an additional method in sc.pp.neighbors
#3831
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Use to build unweighted adjacency matrix.\nFilter out zeros while creating matrix.
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Hi! Sorry we didn’t react for so long! This looks very nice! Great addition and implementation! |
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+ Coverage 76.77% 76.79% +0.02%
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flying-sheep
changed the title
jaccard as an additional method in sc.pp.neighborsjaccard as an additional method in sc.pp.neighbors
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Thank you for looking over it and fixing it up! And no worries about the delayed response - I know how busy things get! |
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Adds
jaccardas amethodinsc.pp.neighborsalongsideumapandgauss. The method performs a weighting of the kNN adjacency graph using Jaccard coefficients between pairs of connected vertices. This is the weighting used in the PhenoGraph package and in Seurat, and it is especially useful to include it here in light of PhenoGraph no longer being actively maintained and thesc.externalAPI being slated for removal, as mentioned in #3828.N.b., the present implementation of the weighting is notably faster than that in PhenoGraph, since it avoids looping over set intersections in favour of sparse matrix operations, but it returns identical results for identical input matrices of kNN indices.
jaccardas an additionalmethodinsc.pp.neighbors#3828umapandgauss)