Construct a k-Nearest Neighbour Graph from Spatial Coordinates.

Builds a sparse adjacency matrix representing the k-nearest neighbour relationships between spots or cells, using Euclidean distance between spatial coordinates.

Usage

kneighbors_graph(
  location,
  n_neighbors,
  platform,
  include_self = FALSE,
  alg = "kd_tree"
)

Arguments

location: A data frame or matrix with columns x and y representing spatial coordinates, and rownames match barcode/cell names.
n_neighbors: Integer value defining the number of neighbours to consider.
platform: Character string being either "Visium" or "ST", specifying the platform of the dataset being analysed. Determines how distance thresholds and adjacency are calculated whereby "Visium" data is handled slightly differently to compensate for the hexagon shape of the spots.
include_self: Boolean logical value stating whether to include self-connections (default = FALSE).
alg: Character string specifying the algorithm to use for nearest neighbour search. Passed to FNN::get.knn() (default = "kd_tree").

Value

A sparse adjacency matrix (dgCMatrix) representing the k-NN graph.

Examples

### HELPER FUNCTION