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 = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "spatNetwDistributions"
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- 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
logical. show plot
- return_plot
logical. return ggplot object
- save_plot
logical. save the plot
- save_param
list of saving parameters, see
showSaveParameters- default_save_name
default save name for saving, don't change, change save_name in save_param
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.