Find Spatial Neighbors

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

A data.table.

Examples

data(mini_giotto_single_cell)

# get all cells
all_cells = slot(mini_giotto_single_cell, 'cell_ID')

# 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])
#>      cell_ID nb_cells
#>  1:   cell_2     both
#>  2:   cell_7     both
#>  3:  cell_12     both
#>  4:  cell_15     both
#>  5:  cell_17   source
#>  6:  cell_30 neighbor
#>  7:  cell_37   others
#>  8:  cell_40   others
#>  9:  cell_44   others
#> 10:  cell_53   others
#> 11:  cell_64   others
#> 12:  cell_74   others
#> 13:  cell_85 neighbor
#> 14:  cell_86   others
#> 15:  cell_90   others
#> 16:  cell_95 neighbor
#> 17:  cell_96 neighbor
#> 18: cell_107 neighbor
#> 19: cell_113 neighbor
#> 20: cell_118   others