calculate_summary_distances_between_cell_types — calculate_summary_distances_between_cell

Returns the mean, median and stardard deviation of the distances between phenotypes

calculate_summary_distances_between_cell_types(
  sce_object,
  column = "Phenotype",
  all_marker_combinations = TRUE,
  combinations_of_interest = NULL
)

Arguments

sce_object	SingleCellExperiment object in the form of the output of format_image_to_sce
column	Column of cells to choose the phenotype from (e.g. Cell.Type, Cell.Type2, etc)
all_marker_combinations	If TRUE, the distances between all possible combinations of markers will be calculated
combinations_of_interest	Vector of marker combinations to consider if all_marker_combinations is FALSE

Value

A data.frame is returned

Examples

summary_distances <- calculate_summary_distances_between_cell_types(SPIAT::formatted_image)
#> [1] "All markers are used in pair-wise distance calculation: "
#> [1] "OTHER"   "AMACR"   "CD3,CD4" "CD3,CD8" "CD3"     "PDL-1"