Build a niche assay based on the profile of neighbouring cells

Build a niche assay based on the profile of neighbouring cells

Usage

getNiche(
  spe,
  at = c("cell", "grid"),
  nbrs_name = NULL,
  group.by,
  use_weight = FALSE
)

Arguments

spe

A SpatialExperiment object

at

Option of cell or grid neighbourhood

nbrs_name

Name of the neighbour list in spe@metadata$grid[[at]]

group.by

Character vector to group neighbours cell by. Should be in either colData(spe) or spe@metadata$grid_density, depending on "at". Multiple groups can be used. See details

use_weight

Whether to scale each nbr based on its weight

Value

A matrix where rows are cells/grid points and cols are groups based on group.by

Details

For numerical group, result will be sum of nbrs for each cell. For categorical group (factor/string), result will be counts of nbrs belonging in category

Examples

data("xenium_bc_spe")

spe <- findNbrsSpatial(spe,k=30)
niche = getNiche(spe,at="cell",group.by="cell_type")