Create shared nearest neighbors graph — createSharedNNGraph.Region • SpatialMap

Function to create a shared nearest neighbors graph, implemented with DBSCAN

Usage

createSharedNNGraph.Region(
  object,
  k,
  kt = NULL,
  jp = FALSE,
  representation = "spatial",
  name = NULL,
  ...
)

object: A Region object
k: The number of nearest neighbors to consider when calculating shared nearest neighbors
kt: The minimum threshold on the number of shared nearest neighbors to build the SNN graph. Edges are only preserved if kt or more neighbors are shared.
jp: Use the definition of SNN by Jarvis and Patrick (1973). Shared neighbors are only counted between points that are in each other's neighborhood. Otherwise 0 is returned.
representation: The name of the representation, with associated cell embeddings, to be used to compute the frNN graph
name: The name of the NN graph. Internal.
...: Additional arguments passed to dbscan::sNN()

Shared nearest neighbors is a K nearest neighbor network that guarantees that all edges are mutual.