findNetworkNeighbors

Find the spatial neighbors for a selected group of cells within the selected spatial network.

findNetworkNeighbors(
  gobject,
  spatial_network_name,
  source_cell_ids = NULL,
  name = "nb_cells"
)

Arguments

gobject

Giotto object

spatial_network_name

name of spatial network

source_cell_ids

cell ids for which you want to know the spatial neighbors

name

name of the results

Value

data.table

Examples

data(mini_giotto_single_cell)
#> Warning: data set ‘mini_giotto_single_cell’ not found

# get all cells
all_cells = slot(mini_giotto_single_cell, 'cell_ID')
#> Error: object 'mini_giotto_single_cell' not found

# find all the spatial neighbours for the first 5 cells
# within the Delaunay network
findNetworkNeighbors(mini_giotto_single_cell,
                     spatial_network_name = 'Delaunay_network',
                     source_cell_ids = all_cells[1:5])
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found