computeSpatialWeights: Compute Spatial Weights for BLISA

In blisa: Infer Cell-Cell Communication from Spatial Transcriptomics

Compute Spatial Weights for BLISA

Description

Builds queen (nearby) and distance-decay (diffuse) spatial weight matrices from a bin-level sf object, excluding bins that have no neighbours.

Usage

computeSpatialWeights(bins, bin_size = 50, dmax = 250)

Arguments

bins	An sf object of spatial bins.
bin_size	Numeric. Bin spacing used to define queen adjacency (1.2 * bin_size radius).
dmax	Numeric. Maximum distance for diffuse-mode neighbours.

Value

A list with:

queen_wt

Spatial weights list for nearby (queen) mode.

dist_wt

Spatial weights list for diffuse (distance-decay) mode.

keep_idx_queen

Integer indices of bins used in queen-mode Moran.

keep_idx_dist

Integer indices of bins used in diffuse-mode Moran.

isolate_idx_queen

Integer indices of original queen-mode isolates.

isolate_idx_dist

Integer indices of original diffuse-mode isolates.

queen_nb_full

Full (unsubset) neighbour list for nearby mode, indexed over all bins.

dist_nb_full

Full (unsubset) neighbour list for diffuse mode, indexed over all bins.

Examples

## Not run: 
set.seed(42)
pts  <- sf::st_as_sf(
  data.frame(x = runif(300, 0, 1000), y = runif(300, 0, 1000)),
  coords = c("x", "y"), crs = NA
)
bins <- sf::st_sf(
  geometry = sf::st_make_grid(pts, cellsize = 100,
                              what = "polygons", square = FALSE)
)
sw <- computeSpatialWeights(bins, bin_size = 100, dmax = 300)
names(sw)

## End(Not run)

blisa documentation built on Oct. 30, 2026, 9:10 a.m.