calculate_entropy: calculate_entropy

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

calculate_entropy

Description

If arg 'radius' is not specified, the function returns the entropy of the cell types of interest for the whole image. If arg 'radius' is specified, the function returns a data frame where each row is a reference cell and the columns stores the entropy of the cell types of interest in each circle of the reference cells.

Usage

calculate_entropy(
  spe_object,
  cell_types_of_interest,
  feature_colname = "Phenotype",
  radius = NULL
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
cell_types_of_interest	String Vector. Cell types of interest. If arg 'radius' is not NULL, the first cell type is considered as reference cell type. Circles of the specified radius will be drawn around the reference cells and the entropy of cell types will be calculated for each of the reference cells.
feature_colname	String specifying the column the cell types are from.
radius	(OPTIONAL) Numeric. The maximum radius around a reference cell for another cell to be considered an interaction.

Value

A dataframe or a number depending on the argument radius

Examples

calculate_entropy(SPIAT::defined_image, 
cell_types_of_interest = c("Immune1","Immune2"),
feature_colname = "Cell.Type")

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