calculate_proportions_of_cells_in_structure: calculate_proportions_of_cells_in_structure

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

calculate_proportions_of_cells_in_structure

Description

Calculate the proportion of cells of interest in each defined tissue structure relative to all cells in each structure and relative to the same cell type in the whole image.

Usage

calculate_proportions_of_cells_in_structure(
  spe_object,
  cell_types_of_interest,
  feature_colname
)

Arguments

spe_object	SpatialExperiment object in the form of the output of format_image_to_spe.
cell_types_of_interest	String Vector of cell types to consider.
feature_colname	String. The name of the column where the cell types of interest are under.

Value

A data.frame

Examples

spe_border <- identify_bordering_cells(SPIAT::defined_image,
reference_cell = "Tumour", feature_colname = "Cell.Type", n_to_exclude = 10)
spe_dist <- calculate_distance_to_margin(spe_border)
spe_structure <- define_structure(spe_dist,
cell_types_of_interest = c("Immune1","Immune2","Immune3"),
feature_colname = "Cell.Type", n_margin_layers = 5)
calculate_proportions_of_cells_in_structure(spe_structure,
cell_types_of_interest = c("Immune1","Immune3"),feature_colname="Cell.Type")

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