spatNetwDistributions

spatNetwDistributionsDistance

Description

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

Usage

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

Argument	Description
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` <#allplotssavefunction>`_
default_save_name	default save name for saving, alternatively change save_name in save_param

Details

The list(“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. list() The list(“k_neighbors”) option shows the number of k neighbors distribution over all cells.

Value

ggplot plot