calculate_summary_distances_of_cells_to_borders: calculate_summary_distances_of_cells_to_borders

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

calculate_summary_distances_of_cells_to_borders

Description

Returns the mean, median and standard deviation of the distances between a specified cell type to the border.

Usage

calculate_summary_distances_of_cells_to_borders(
  spe_object,
  cell_types_of_interest,
  feature_colname = "Cell.Type"
)

Arguments

spe_object	SpatialExperiment object. It should contain information of tissue structure and cell distances to the tissue region border ('colData()' has 'Region' and 'Distance.To.Border' columns).
cell_types_of_interest	String Vector of cell types to consider.
feature_colname	String specifying which column the interested cell types are from.

Value

A data.frame is returned

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_summary_distances_of_cells_to_borders(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.