Histogram of Distance Distribution for Spatial k-Neighbors

spatNetwDistributions()

This function return histograms displaying the distance distribution for each spatial k-neighbor.

spatNetwDistributions(
    gobject,
    spatial_network_name = "spatial_network",
    distribution = c("distance", "k_neighbors"),
    hist_bins = 30,
    test_distance_limit = NULL,
    ncol = 1,
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "spatNetwDistributions"
)

Arguments

gobject	Giotto object
spatial_network_name	name of spatial network
distribution	show the distribution of cell-to-cell distance or number of k neighbors
hist_bins	number of binds to use for the histogram
test_distance_limit	effect of different distance threshold on k-neighbors
ncol	number of columns to visualize the histograms in
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters from all_plots_save_function()
default_save_name	default save name for saving, alternatively change save_name in save_param

Value

A ggplot.

Details

The distance option shows the spatial distance distribution for each nearest neighbor rank (1st, 2nd, 3th, … neighbor). With this option the user can also test the effect of a distance limit on the spatial network. This distance limit can be used to remove neighbor cells that are considered to far away. The k_neighbors option shows the number of k neighbors distribution over all cells