calculate_cross_functions: calculate_cross_functions

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

calculate_cross_functions

Description

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

Usage

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

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
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)

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.