number_of_cells_within_radius — number_of_cells_within_radius • SPIAT

Calculates the number of cells of a target cell type within a pre-defined radius around cells of a reference cell type.

Usage

number_of_cells_within_radius(
  sce_object,
  reference_celltype,
  target_celltype,
  radius = 20,
  feature_colname
)

Arguments

sce_object: SingleCellExperiment object in the form of the output of format_image_to_sce.
reference_celltype: String. Cell type to be used for reference cells.
target_celltype: String. Cell type to be used for target cells.
radius: Numeric. Radius around the reference cells.
feature_colname: String specifying the column with the desired cell type annotations.

Value

A list of dataframes with the number of target cells of each of the reference cells

Examples

n_in_radius <- number_of_cells_within_radius(SPIAT::defined_image,
reference_celltype = "Tumour", target_celltype="Immune1", radius = 50,
feature_colname = "Cell.Type")