R/lrr_plot.R

In gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

#' Prepare log relative risk values for plotting with a diverging color palette
#'
#' Internal function to convert an object of class 'im' to values readable by \code{\link[fields]{image.plot}} function within the \code{\link{rrs}} and \code{\link{lotrrs}} functions.
#'
#' @param input An object of class 'rrs' from the \code{\link{rrs}} or \code{\link{lotrrs}} function.
#' @param plot_cols Character string of length three (3) specifying the colors for plotting: 1) numerator, 2) insignificant, and 3) denominator from the \code{\link{rrs}} or \code{\link{lotrrs}}  function.
#' @param midpoint Numeric. The value to center the diverging color palette.
#' @param lower_lrr Numeric. The lower value to concatenate the color key. The default (NULL) uses the minimum value from \code{input}.
#' @param upper_lrr Numeric. The upper value to concatenate the color key. The default (NULL) uses the maximum value from \code{input}.
#' @param digits Integer. The number of significant digits for the labels using the \code{round} function (default is 1).
#'
#' @return An object of class 'list'. This is a named list with the following components:
#'
#' \describe{
#' \item{\code{v}}{An object of class 'SpatRaster' for the estimated gating surface.}
#' \item{\code{cols}}{An object of class 'vector', returns diverging color palette values.}
#' \item{\code{breaks}}{An object of class 'vector', returns diverging color palette breaks.}
#' \item{\code{at}}{An object of class 'vector', returns legend breaks.}
#' \item{\code{labels}}{An object of class 'vector', returns legend labels.}
#' }
#'
#' @importFrom grDevices colorRampPalette
#' @importFrom terra rast values
#' @export
#'
#' @keywords internal
#' 
lrr_plot <- function(input,
                     cols,
                     midpoint = 0,
                     lower_lrr = NULL,
                     upper_lrr = NULL,
                     digits = 1) {

  # Inputs
  if (!inherits(input, "im")) {
    stop("The 'input' argument must be an object of class 'im'")
  }

  if (length(cols) != 3) {
    stop("The 'cols' argument must be a vector of length 3")
  }

  out <- terra::rast(input)  # create SpatRaster

  min_raw_value <- min(terra::values(out)[is.finite(terra::values(out))], na.rm = TRUE) # minimum absolute value of SpatRaster
  max_raw_value <- max(terra::values(out)[is.finite(terra::values(out))], na.rm = TRUE) # maximum absolute value of SpatRaster
  
  # Restrict spurious log relative risk values
  if (!is.null(lower_lrr)) {
    if (lower_lrr >= 0) {
      stop("The 'lower_lrr' argument must be a numeric value less than zero")
    }
    terra::values(out)[terra::values(out) <= lower_lrr] <- lower_lrr
  }
  if (!is.null(upper_lrr)) {
    if (upper_lrr <= 0) {
      stop("The 'upper_lrr' argument must be a numeric value greater than zero")
    }
    terra::values(out)[terra::values(out) >= upper_lrr] <- upper_lrr
  }

  # Identify ramp above and below midpoint
  lowerhalf <- length(terra::values(out)[terra::values(out) < midpoint & !is.na(terra::values(out))]) # values below 0
  upperhalf <- length(terra::values(out)[terra::values(out) > midpoint & !is.na(terra::values(out))]) # values above 0
  min_absolute_value <- min(terra::values(out)[is.finite(terra::values(out))], na.rm = TRUE) # minimum absolute value of raster
  max_absolute_value <- max(terra::values(out)[is.finite(terra::values(out))], na.rm = TRUE) # maximum absolute value of raster

  # Color ramp parameters
  ## Colors
  ### vector of colors for values below midpoint
  rc1 <- grDevices::colorRampPalette(colors = c(cols[3], cols[2]), space = "Lab")(lowerhalf)
  ### vector of colors for values above midpoint
  rc2 <- grDevices::colorRampPalette(colors = c(cols[2], cols[1]), space = "Lab")(upperhalf)
  ### compile colors
  rampcols <- c(rc1, rc2)
  ## Breaks
  ### vector of breaks for values below midpoint
  rb1 <- seq(min_absolute_value, midpoint, length.out = lowerhalf + 1)
  ### vector of breaks for values above midpoint
  rb2 <- seq(midpoint, max_absolute_value, length.out = upperhalf + 1)[-1]
  ### compile breaks
  rampbreaks <- c(rb1, rb2)

  # At for colorkey lables
  rbr <- max_absolute_value - min_absolute_value
  rbt <- rbr / 4
  rbs <- seq(min_absolute_value, max_absolute_value, rbt)
  rbm <- which.min(abs(rbs - midpoint))
  rbs[rbm] <- midpoint

  # Text for colorkey labels
  rbl <- round(rbs, digits = digits)
  
  if (min_raw_value < min_absolute_value) { rbl[1] <- paste("<", rbl[1], sep = "") }
  
  if (max_raw_value > max_absolute_value) { rbl[5] <- paste(">", rbl[5], sep = "") }

  # Output
  out <- list("v" = out,
              "cols" = rampcols,
              "breaks" = rampbreaks,
              "at" = rbs,
              "labels" = rbl)
}