Build the neighbourhood kernels

Returns the per-cell kernel-weighted neighbour abundances: the Gaussian biological kernel K_bio (used for the proximity coefficients) and the short-range exponential technical kernel K_tech. Useful for inspecting the neighbourhood before or independently of a fit.

Usage

buildNeighbourhood(object, ...)

# S4 method for class 'SpatialExperiment'
buildNeighbourhood(
  object,
  celltype_col,
  h_bio = 30,
  h_tech = 5,
  eps = NULL,
  ...
)

Arguments

object

A SpatialExperiment::SpatialExperiment.

...

Passed to the kernel builder.

celltype_col

colData column with the cell-type annotation.

h_bio, h_tech

Bandwidths in micrometres (defaults 30, 5).

eps

Truncation radius; defaults to 3 * h_bio.

Value

A list with K_bio and K_tech (cells x cell types).

Examples

spe <- readRDS(system.file("extdata", "bc_xenium_subset.rds", package = "PACE"))
nb <- buildNeighbourhood(spe, celltype_col = "cellType")
dim(nb$K_bio)
#> [1] 7898    8