Construct a distance-based neighbour list from cell coordinates.

Usage

findNbrsSpatial(
  spe,
  k = NULL,
  radius = NULL,
  dist_func = c("idw", "exp", "binary", "none"),
  standardisation = c("none", "row"),
  scale = 1,
  nbrs_name = NULL,
  cpu_threads = 6
)

Arguments

spe: A SpatialExperiment object.
k: Integer scalar for number of nearest neighbours to find. Can be used with radius. See details.
radius: Numeric for maximum distance to search for neighbours. Can be with k. See details
dist_func: Options for distance-based weight. "idw" for inverse distance, "exp" for exponential decay, "binary" for constant weight, and "none" for raw euclidean distance.
standardisation: Options for weight standardisation. "none" for nothing, and "row" for dividing weights by number of neighbours.
scale: Numeric scaler for weight scaling.
nbrs_name: Name of the neighbour list to be stored. Default to be "spatial".
cpu_threads: Number of cpu threads for parallel computation.

Value

A SpatialExperiment object with neighbour list stored in spe@metadata$nbrs$cell[[nbrs_name]]

Details

if only k is provided, neighbours are found using findKNN. If only radius is provided, neighbours are found using findNeighbors. If both are provided, then knn is done first then neighbours are filtered to only those within radius.

Examples


data("xenium_bc_spe")
spe <- findNbrsSpatial(spe,k=20,radius=100)