Cross-adjacency matrix with feature weighting

Usage

cross_weighted_spatial_adjacency(
  coord_mat1,
  coord_mat2,
  feature_mat1,
  feature_mat2,
  wsigma = 0.73,
  alpha = 0.5,
  nnk = 27,
  maxk = nnk,
  weight_mode = c("binary", "heat"),
  sigma = 1,
  dthresh = sigma * 2.5,
  normalized = TRUE
)

Arguments

coord_mat1: the first coordinate matrix (the query)
coord_mat2: the second coordinate matrix (the reference)
feature_mat1: the first feature matrix
feature_mat2: the second feature matrix
wsigma: the sigma for the feature heat kernel
alpha: the mixing weight for the spatial distance (1=all spatial weighting, 0=all feature weighting)
nnk: the maximum number of spatial nearest neighbors to include
maxk: the maximum number of neighbors to include within spatial window
weight_mode: the type of weighting to use: "binary" or "heat" (default: "binary")
sigma: the spatial sigma for the heat kernel weighting (default: 1)
dthresh: the threshold for the spatial distance
normalized: whether to normalize the rows to sum to 1

Value

A sparse cross-graph adjacency matrix of feature-weighted spatial similarities.

Examples

set.seed(123)
coords <- as.matrix(expand.grid(1:5, 1:5))
fmat1 <- matrix(rnorm(5*25), 25, 5)
fmat2 <- matrix(rnorm(5*25), 25, 5)

adj <- cross_weighted_spatial_adjacency(coords, coords, fmat1, fmat2)