scSpatialSIM (version 0.1.3.4)

GenerateHoles: Generate holes in a spatial simulation object

Description

This function generates holes (regions of low probability) in a spatial simulation object based on user-defined parameters. The function uses a kernel density estimate to simulate holes, and returns a modified version of the input object with the holes added. The function also has options to compute a density heatmap and to assign points within the holes to be dropped or kept based on a scaled probability value.

Usage

GenerateHoles(
  sim_object,
  xmin = NA,
  xmax = NA,
  ymin = NA,
  ymax = NA,
  sdmin = 1/2,
  sdmax = 2,
  hole_prob = c(0.2, 0.35),
  force = FALSE,
  density_heatmap = FALSE,
  step_size = 1,
  cores = 1,
  overwrite = FALSE,
  use_window = FALSE
)

Value

A modified spatial simulation object with holes added

Arguments

sim_object

A spatial simulation object of class SpatSimObj

xmin

Minimum x-coordinate for the holes (default: NA)

xmax

Maximum x-coordinate for the holes (default: NA)

ymin

Minimum y-coordinate for the holes (default: NA)

ymax

Maximum y-coordinate for the holes (default: NA)

sdmin

Minimum standard deviation for the kernels (default: 1/2)

sdmax

Maximum standard deviation for the kernels (default: 2)

hole_prob

A vector of length 2 with the minimum and maximum probabilities of a point being within a hole (default: c(0.2, 0.35))

force

Logical; if TRUE, forces the function to simulate outside the window boundaries (default: FALSE)

density_heatmap

Logical; if TRUE, computes a density heatmap (default: FALSE)

step_size

The step size for the grid (default: 1)

cores

The number of cores to use for parallel processing (default: 1)

overwrite

boolean to replace holes if they have been simulated previously

use_window

boolean whether to use the simulation window to set x and y limits

Details

The function first checks that the input object is of the correct class, and that no parameters are NULL. If any parameters are NULL, the function stops with an error message. If the x- and y-ranges for the holes extend beyond the boundaries of the simulation window, the function also stops with an error message, unless the force parameter is set to TRUE. The function then produces kernel parameter lists for each simulated pattern, and generates a grid based on the user-defined step size. If density_heatmap is set to TRUE, the function computes a density heatmap using the CalculateGrid function. Finally, the function computes hole probabilities for each simulated pattern, assigns each point to be dropped or kept based on a scaled probability value, and returns the modified simulation object.

Examples

sim_object <- CreateSimulationObject()

#simulate points
sim_object <- GenerateSpatialPattern(sim_object, lambda = 20)

# Generate tissue with default parameters
sim_object <- GenerateTissue(sim_object)

# Generate holes in the simulation object
sim_object <- GenerateHoles(sim_object, hole_prob = c(0.1, 0.3), force = TRUE)