vignettes/tut8_giotto_grid_network.Rmd
tut8_giotto_grid_network.Rmd\(~\)
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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# 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')