Description Usage Arguments Value
Function to convert the knn graph into the snn graph. Stored in a sparse representation.
1 2 | CalcSNNSparse(cell.names, k.param, nn.large, nn.ranked, prune.SNN,
print.output)
|
cell.names |
A vector of cell names which will correspond to the row/ column names of the SNN |
k.param |
Defines nearest neighborhood when computing NN graph |
nn.large |
Full KNN graph (computed with get.knn with k set to k.param * k.scale) |
nn.ranked |
Subset of full KNN graph that only contains the first k.param nearest neighbors. Used to define Jaccard distances between any two cells |
prune.SNN |
Sets the cutoff for acceptable Jaccard distances when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 — no pruning, 1 — prune everything). |
print.output |
Whether or not to print output to the console |
Returns an adjacency matrix representation of the SNN graph
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