Compute the spatial adjacency matrix for a coordinate matrix

This function computes the spatial adjacency matrix for a given coordinate matrix using specified parameters. Adjacency is determined by distance threshold and the maximum number of neighbors.

Usage

spatial_adjacency(
  coord_mat,
  dthresh = sigma * 3,
  nnk = 27,
  weight_mode = c("binary", "heat"),
  sigma = 5,
  include_diagonal = TRUE,
  normalized = TRUE,
  stochastic = FALSE,
  handle_isolates = c("self_loop", "keep_zero", "drop")
)

Arguments

coord_mat

A numeric matrix representing the spatial coordinates

dthresh

Numeric, the distance threshold defining the radius of the neighborhood (default is sigma*3)

nnk

Integer, the maximum number of neighbors to include in each spatial neighborhood (default is 27)

weight_mode

Character, the mode for computing weights, either "binary" or "heat" (default is "binary")

sigma

Numeric, the bandwidth of the heat kernel if weight_mode == "heat" (default is 5)

include_diagonal

Logical, whether to assign 1 to diagonal elements (default is TRUE)

normalized

Logical, whether to make row elements sum to 1 (default is TRUE)

stochastic

Logical, whether to make column elements also sum to 1 (only relevant if normalized == TRUE) (default is FALSE)

handle_isolates

How to treat zero-degree nodes when normalizing: "self_loop" adds a self-loop (default), "keep_zero" leaves them as zero, or "drop" removes them from the matrix.

Value

A sparse symmetric matrix representing the computed spatial adjacency

Examples

coord_mat = as.matrix(expand.grid(x=1:6, y=1:6))
sa <- spatial_adjacency(coord_mat)