scSpatialSIM (version 0.1.3.4)

GenerateDistributions: Generate Characteristic Distributions of Cells

Description

Generate Characteristic Distributions of Cells

Usage

GenerateDistributions(
  spatial_data,
  positive_mean = 10,
  negative_mean = 2,
  positive_sd = 2,
  negative_sd = 1
)

Value

object with a class that is the same as input spatial_data with new columns containing distributions for positive/negative assigned cells

Arguments

spatial_data

object of either class list or data.frame. Can be created from SpatSimObj with CreateSpatialList

positive_mean, negative_mean

number for mean of which to center the distribution of the positive and negative cell types. Can be single number of vector with length matching number of Cells.

positive_sd, negative_sd

number for the standard deviation around the positive cell type mean. Can be single value or same length as number of Cells.

Examples

#create simulation object
spatial_data = CreateSimulationObject(sims = 1, cell_types = 1) %>%
  #produce the point pattern
  GenerateSpatialPattern() %>%
  #make tissues
  GenerateTissue(density_heatmap = FALSE, step_size = 0.1, cores = 1) %>%
  #create positive and negative cells
  GenerateCellPositivity(k = 4, sdmin = 3, sdmax = 5,
  density_heatmap = FALSE, step_size = 1, cores = 1, probs = c(0.0, 0.1), shift = 0) %>%
  #convert to a list of spatial data frames
  CreateSpatialList(single_df = FALSE)
spat_data_distribution = GenerateDistributions(spatial_data)