calculate_cross_functions — calculate_cross

Compute and plot the cross functions between two specified cell types. This function implements the cross functions from [spatstat] package.

Usage

calculate_cross_functions(
  sce_object,
  method = "Kcross",
  cell_types_of_interest,
  feature_colname,
  plot_results = TRUE,
  dist = NULL
)

Arguments

sce_object: SingleCellExperiment object in the form of the output of format_image_to_sce.
method: String that is the method for dependence calculation. Options: "Gcross", "Kcross", "Kcross.inhom", "Lcross", "Jcross". Default method is "Kcross".
cell_types_of_interest: String Vector. Cell types of interest.
feature_colname: String that is the name of the column of the types.
plot_results: Boolean. TRUE if result to be plotted, FALSE if not. In either case, an object with the results is returned
dist: Number (OPTIONAL) The largest distance between two cell types at which K function is evaluated. If NULL, use the default distances set by cross functions.

Value

An object of class "fv" defined in `spatstat` package.

Examples

df_cross <- calculate_cross_functions(SPIAT::defined_image, method = "Kcross",
              cell_types_of_interest = c("Tumour","Immune3"),
              feature_colname ="Cell.Type", dist = 100)