Construct a neighbour list from grid coordinates.

Usage

findNbrsGrid(
  spe,
  n = 1,
  radius = NULL,
  diagonal = FALSE,
  dist_func = c("idw", "exp", "binary", "none"),
  dist_type = c("euclidean", "manhattan"),
  standardisation = c("row", "none"),
  scale = 1,
  nbrs_name = NULL,
  cpu_threads = 6
)

Arguments

spe: A SpatialExperiment object.
n: Integer. Search for neighbours within (...). Either the number of neighbors or radius
radius: Numeric. Search for neighbours within the radius.
diagonal: Whether to consider diagonal connection if using square grid
dist_func: Options for distance-based weight. "idw" for inverse distance, "exp" for exponential decay, "binary" for constant weight, and "raw" for raw distance.
dist_type: Options of using euclidean or manhattan for distance calculation
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 "grid".
cpu_threads: Number of cpu threads for parallel computation.

Value

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

Details

If n is used, distance is scaled to unit distance

Examples


data("xenium_bc_spe")
spe <- gridDensity(spe)
spe <- findNbrsGrid(spe,n=3)