spatNetwDistributionsDistance

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

ggplot plot

Details

The distance option shows the spatial distance distribution for each nearest neighbor rank (1st, 2nd, 3th, ... neigbor). 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 neigbor cells that are considered to far away.
The k_neighbors option shows the number of k neighbors distribution over all cells.