computes shared nearest neighbors from embedding.
Arguments
- x
A numeric matrix (with features as columns and items as rows) from which nearest neighbors will be computed.
- k
The number of nearest neighbors.
- type
A string specifying the type of weighting scheme to use for shared neighbors. Possible choices include "rank", "number", and "jaccard". See
typeinbluster::neighborsToSNNGraph()for details.- BNPARAM
A BiocNeighbors parameter object to compute kNNs. Ignored unless the input is a matrix or data.frame. If omitted, the Annoy approximation will be used if there are more than 500 elements.
Examples
d1 <- mockData()
emb2snn(as.matrix(d1[,seq_len(2)]),k=5)
#> IGRAPH a5be2b9 U-W- 40 261 --
#> + attr: weight (e/n)
#> + edges from a5be2b9:
#> [1] 1-- 2 1-- 4 2-- 4 3-- 5 3-- 6 1-- 7 4-- 7 3-- 8 6-- 8 1-- 8
#> [11] 6-- 9 8-- 9 1-- 9 3-- 9 3--10 5--10 5--11 10--11 3--11 2--12
#> [21] 4--12 1--12 7--12 3--13 6--13 8--13 9--13 5--14 10--14 11--14
#> [31] 3--14 5--15 10--15 11--15 14--15 3--15 5--16 11--16 14--16 15--16
#> [41] 10--16 3--16 6--17 9--17 13--17 8--17 3--17 1--18 4--18 7--18
#> [51] 12--18 2--18 3--19 13--19 6--19 8--19 17--19 9--19 10--20 3--20
#> [61] 5--20 11--20 14--20 15--20 16--20 1--20 18--20 8--20 9--20 6--20
#> [71] 13--21 17--21 7--21 6--21 9--21 19--21 8--21 3--22 6--22 8--22
#> + ... omitted several edges