R/average_marker_intensity_within_radius.R

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

#' average_marker_intensity_within_radius
#'
#' @description Calculates the average intensity of the target_marker within a
#'   radius from the cells positive for the reference marker. Note that it pools
#'   all cells with the target marker that are within the specific radius of any
#'   reference cell. Results represent the average intensities within a radius,
#'   but not a vector of metrics for each cell. 
#'
#' @param spe_object SpatialExperiment object in the form of the output of
#'   \code{\link{format_image_to_spe}}.
#' @param reference_marker String specifying the marker that is used for
#'   reference cells.
#' @param target_marker String specifying the marker to calculate its average
#'   intensity.
#' @param radius Numeric specifying the radius of search for cells around the
#'   reference cells.
#' @import dplyr
#' @return A single number is returned
#' @examples
#' average_marker_intensity_within_radius(SPIAT::simulated_image,
#'                                        reference_marker ="Immune_marker3",
#'                                        target_marker = "Immune_marker2",
#'                                        radius=30)
#' @export

average_marker_intensity_within_radius <- function(spe_object, 
                                                   reference_marker, 
                                                   target_marker, 
                                                   radius = 20){
    formatted_data <- bind_info(spe_object)

    #Select the cells that have the reference marker phenotype
    reference_cells <- formatted_data[grepl(reference_marker, 
                                            formatted_data$Phenotype),]
    if (nrow(reference_cells) == 0) {
        stop("There are no reference cells found for the marker")
    }
    #Target cells are don't contain the reference marker
    target_cells <- formatted_data[grepl(target_marker, formatted_data$Phenotype),]
    if (nrow(target_cells) == 0) {
        stop("There are no target cells found for the marker")
    }
    
    #Remove cells with both markers
    common_cells <- reference_cells$Cell.ID[reference_cells$Cell.ID 
                                            %in% target_cells$Cell.ID]
    reference_cells <- reference_cells[!(reference_cells$Cell.ID 
                                         %in% common_cells),]
    target_cells <- target_cells[!(target_cells$Cell.ID %in% common_cells),]

    #Get the coordinates to find neighbours
    reference_cell_cords <- reference_cells[,c("Cell.X.Position", 
                                               "Cell.Y.Position")]
    target_cell_cords <- target_cells[,c("Cell.X.Position", "Cell.Y.Position")]

    #frNN output ids, the rowid of reference_cell_cords matches the row number of target_cell_cords
    search_result <- dbscan::frNN(target_cell_cords, eps = radius, 
                                  query = reference_cell_cords, sort = FALSE)
    rownums <- unique(unlist(search_result$id))

    #check
    if (length(rownums) == 0) {
        stop("There are no target cells within the specified radius, cannot calculate average intensity")
    } else {
        target_within_radius <- target_cells[rownums,]
        average_marker_intensity <- mean(target_within_radius[,target_marker], 
                                         na.rm=TRUE)}
    return(average_marker_intensity)
}