Spatial grid or network

library(Giotto)
data("mini_giotto_single_cell")

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1. Create a spatial grid

mini_giotto_single_cell <- createSpatialGrid(gobject = mini_giotto_single_cell,
                                            sdimx_stepsize = 250,
                                            sdimy_stepsize = 250,
                                            minimum_padding = 50)
# visualize grid
spatPlot(gobject = mini_giotto_single_cell, show_grid = T, point_size = 1.5)

# create another larger grid
mini_giotto_single_cell <- createSpatialGrid(gobject = mini_giotto_single_cell,
                                            sdimx_stepsize = 350,
                                            sdimy_stepsize = 350,
                                            minimum_padding = 50, 
                                            name = 'large_grid')

# show available grids
showGrids(mini_giotto_single_cell)

# visualize other grid
spatPlot2D(gobject = mini_giotto_single_cell, point_size = 1.5, 
           show_grid = T, spatial_grid_name = 'large_grid')

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2. Create a spatial network

# get information about the Delaunay network
plotStatDelaunayNetwork(gobject = mini_giotto_single_cell, maximum_distance = 400)

# create a spatial network, the Delaunay network is the default network
# default name = 'Delaunay_network'
mini_giotto_single_cell = createSpatialNetwork(gobject = mini_giotto_single_cell, minimum_k = 2, 
                                    maximum_distance_delaunay = 400)

# create a kNN network with 4 spatial neighbors
# default name = 'kNN_network'
mini_giotto_single_cell = createSpatialNetwork(gobject = mini_giotto_single_cell, minimum_k = 2, 
                                    method = 'kNN', k = 4)

# show available networks
showNetworks(mini_giotto_single_cell)

# visualize the two different spatial networks  
spatPlot(gobject = mini_giotto_single_cell, show_network = T,
         network_color = 'blue', spatial_network_name = 'Delaunay_network',
         point_size = 2.5, cell_color = 'cell_types')

spatPlot(gobject = mini_giotto_single_cell, show_network = T,
         network_color = 'blue', spatial_network_name = 'kNN_network',
         point_size = 2.5, cell_color = 'cell_types')