Calculate Colocalization — cell_pair_presence • spacedeconv

Calculate Colocalization

Usage

cell_pair_presence(
  spe,
  method = NULL,
  distance = 0,
  cell_type_A = NULL,
  cell_type_B = NULL,
  niter = 100,
  presence_matrix = NULL,
  threshold = NULL
)

Arguments

spe: SpatialExperiment
method: presence method
distance: distance in spot diameter
cell_type_A: celltype 1
cell_type_B: celltype 2
niter: permutations
presence_matrix: presence matrix if available
threshold: threshold for custom presence determination

Value

presence/absence for each cell type