R/visualize_phyloregions.R

In phyloregion: Biogeographic Regionalization and Macroecology

color_key <- function(y, cols, vals, lab = "ED", leg = 5, lwd = 15,
                      pos = "bottomright") {
  if (pos == "bottomright") {
    a <- y@bbox[3] + 0.5
    b <- y@bbox[2]
  }
  if (pos == "topleft") {
    a <- y@bbox[1] - 0.5
    b <- y@bbox[4] - leg
  }
  if (pos == "bottomleft") {
    a <- y@bbox[1] - 0.5
    b <- y@bbox[2]
  }
  if (pos == "topright") {
    a <- y@bbox[3] + 0.5
    b <- y@bbox[4] - leg
  }
  l <- length(cols)
  x <- cbind(rep(a, l), rep(a, l))
  y <- b + cbind(0:(l - 1) / l, seq_len(l) / l) * (leg)
  for (i in seq_len(l)) lines(x[i, ], y[i, ], col = cols[i], lwd = lwd,
                              lend = 2)
  text(x = a, y = b, round(min(vals), 3), pos = 4, cex = 0.7) # lim texts
  text(x = a, y = b + (leg / 2), round(stats::median(vals), 3), pos = 4, cex = 0.7)
  text(x = a, y = b + leg, round(max(vals), 3), pos = 4, cex = 0.7)
  text(x = a, y = b + leg, lab, pos = 3, cex = 1)
}

#' Visualize biogeographic patterns
#'
#' @param x an object of class phyloregion from \code{phyloregion}
#' @param palette name of the palette to generate colors from. The default,
#' \dQuote{NMDS}, allows display of phyloregions in multidimensional
#' scaling color space matching the color vision of the human visual
#' system. The name is matched to the list of available color palettes from
#' the \code{hcl.colors} function in the \code{grDevices} package.
#' @param col vector of colors of length equal to the number of phyloregions.
#' @param pol a polygon shapefile of grid cells.
#' @param label Logical, whether to print cluster names or not
#' @param \dots arguments passed among methods.
#' @return No return value, called for plotting.
#' @rdname plot.phyloregion
#' @importMethodsFrom terra plot
#' @importMethodsFrom terra text
#' @method plot phyloregion
#' @importFrom graphics plot plot.default
#' @rawNamespace export(plot.phyloregion)
#' @export
plot.phyloregion <- function(x, pol = NULL, palette = "NMDS",
                             col = NULL, label = FALSE, ...) {
  if (!inherits(x, "phyloregion"))
    stop("object \"x\" is not of class \"phyloregion\"")
  if(is.null(pol)) pol <- x$pol
  if(is.null(pol)) stop("Need vector polygon!")
  k <- x$k
  #l <- length(shp$cluster)
  if(is.null(col)){
    if(palette=="NMDS") col <- pol$COLOURS
    else col <- hcl.colors(k, palette)[pol$cluster]
  }
  else{
    if(length(col)==k) col <- col[pol$cluster]
    else stop("Expect 'col' of length x$k!")
  }
  plot(pol, "cluster", col = col, ...)
  if (label == TRUE) text(pol, labels = as.character(pol$cluster), ...)
}

#' @rdname plot.phyloregion
#' @export
plot_NMDS <- function(x, ...) {
  if (!inherits(x, "phyloregion"))
    stop("object \"x\" is not of class \"phyloregion\"")
  c1 <- x$NMDS
  plot(c1$points, bg = hexcols(c1), pch = 21, ...)
}

#' @rdname plot.phyloregion
#' @examples
#' library(terra)
#' data(africa)
#' tree <- africa$phylo
#' x <- africa$comm
#' p <- vect(system.file("ex/sa.json", package = "phyloregion"))
#'
#' subphy <- match_phylo_comm(tree, x)$phy
#' submat <- match_phylo_comm(tree, x)$com
#'
#' pbc <- phylobeta(submat, subphy)
#' y <- phyloregion(pbc[[1]], pol=p)
#'
#' plot_NMDS(y, cex=6)
#' text_NMDS(y, cex=2)
#' plot(y, cex=1, palette="NMDS")
#' plot(y, cex=1)
#' @export
text_NMDS <- function(x, ...) {
  if (!inherits(x, "phyloregion"))
    stop("object \"x\" is not of class \"phyloregion\"")
  c1 <- x$NMDS
  text(c1$points, as.character(1:c1$nobj), ...)
}