average_percentage_of_cells_within_radius

Source: R/average_percentage_of_cells_within_radius.R

Calculates the average percentage of cells of a target phenotype within a radius from the cells with a reference phenotype. The calculation is done per reference cell, so runtime will depend on the number of reference cells present. Output is a single value (the mean for the image).

average_percentage_of_cells_within_radius(
  sce_object,
  reference_phenotypes,
  target_phenotypes,
  radius = 100,
  column
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce
reference_phenotypes

String specifying the phenotypes of reference cells
target_phenotypes

String specifying the phenotypes for target cells
radius

Integer specifying the radius of search for cells around the reference cells. Radii of ~100 are recommended. If too small, too few cells might be present
column

String specifying the column with the desired cell type annotations

Value

A numeric vector ard a plot are returned