findNetworkNeighbors: findNetworkNeighbors

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

findNetworkNeighbors

Description

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

Usage

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)

# 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])

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.