R/seq_plot.R

In envi: Environmental Interpolation using Spatial Kernel Density Estimation

#' Prepare an 'im' or 'SpatRaster' object for plotting with sequential color palette
#' 
#' Internal function to convert 'im' object or 'SpatRaster' object to values readable by \code{\link[fields]{image.plot}} function within the \code{\link{plot_perturb}} function. 
#' 
#' @param input An object of class 'im' or 'SpatRaster' from the \code{\link{perlrren}} function.
#' @param plot_cols Character string of length three (3) specifying the colors for plotting: 1) presence, 2) neither, and 3) absence from the \code{\link{plot_obs}} function. 
#' @param thresh_up 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{\link[base]{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 'vector' for the estimated ecological niche values.}
#' \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
#' 
#' @keywords internal
#' 
seq_plot <- function(input,
                     cols,
                     thresh_up = NULL,
                     digits = 1) {
  
  # Inputs
  if (inherits(input, "im")) {
    out <- terra::rast(input)
  } else { out <- input }
  
  max_raw_value <- max(out[is.finite(out)], na.rm = TRUE) # maximum absolute value of SpatRaster
  
  # Restrict spurious standard deviation values
  if (!is.null(thresh_up)) {
    if (thresh_up <= 0) {
      stop("The 'thresh_up' argument must be a numeric value greater than zero")
    }
    out[out >= thresh_up] <- thresh_up
  }
  
  max_absolute_value <- max(out[is.finite(out)], na.rm = TRUE) # maximum absolute value of SpatRaster
  ncols <- length(out[!is.na(out)]) # number of values 
  
  ## Colors
  rampcols <- grDevices::colorRampPalette(colors = c(cols[2], cols[1]), space = "Lab")(ncols)
  
  ## Breaks
  rampbreaks <- seq(0, max_absolute_value, length.out = length(rampcols) + 1)
  
  # At for colorkey lables
  rbr <- max_absolute_value
  rbt <- rbr / 4
  rbs <- seq(0, max_absolute_value, rbt)
  
  # Text for colorkey labels
  rbl <- round(rbs, digits = digits)
  
  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)
}