spatNetwDistributions#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_structures.R#L210

Description#

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

Usage#

spatNetwDistributions(
  gobject,
  spat_unit = NULL,
  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

spat_unit

spatial unit

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_f unction <#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