R/plot_average_intensity.R

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

#' plot_average_intensity
#'
#' @description Takes in a vector or radii and calculates the average intensity
#'   of a target marker using average_intensity function. It plots the intensity
#'   level as a line graph.
#'
#' @param spe_object SpatialExperiment object in the form of the output of
#'   \code{\link{format_image_to_spe}}.
#' @param reference_marker String specifying the reference marker.
#' @param target_marker String specifying the marker to calculate its average
#'   intensity.
#' @param radii Numeric Vector specifying the search radius around reference
#'   cells.
#' @import ggplot2
#' @return A plot is returned
#' @examples
#' plot_average_intensity(SPIAT::simulated_image, reference_marker="Immune_marker3", 
#' target_marker="Immune_marker2", c(30, 35, 40, 45, 50, 75, 100))
#' @export

plot_average_intensity <- function(spe_object, reference_marker, target_marker, radii) {

    average_intensity_result <- vector()

    for (radius in radii) {
        result <- average_marker_intensity_within_radius(spe_object, reference_marker, target_marker, radius = radius)
        #check
        if(!is.numeric(result)) {
            stop(sprintf("Cannot calculate average intensity for radius = %.2f", radius))
        }
        average_intensity_result <- c(average_intensity_result, result)
    }

    average_intensity_df <- data.frame(radii, average_intensity_result)

    p <- ggplot(data=average_intensity_df, aes(x=radii, y=average_intensity_result))

    title <- paste("Average intensity of ", target_marker, " from ", reference_marker, " for various radii", sep="")
    p <- p + geom_line() + geom_point() + ggtitle(title) + xlab("Radius") + ylab("Average Intensity")
    p <- p + theme_bw()
    p
}