R/plot_isospace.R

In ahasverus/SampleSim: Sample Size Effects in Stable Isotope Mixing Solutions

#' Plot data in the isotope space
#' 
#' @description 
#' This function represents the data in the isotope space to overlay consumer 
#' and sources isotope values. User can also use the [MixSIAR::plot_data()].
#'
#' @param filename a character of length 1. The name of the plot file to save.
#' 
#' @param plot_save_pdf a logical value. If `TRUE`, the plot is saved as pdf.
#' 
#' @param plot_save_png a logical value. If `TRUE`, the plot is saved as png.
#' 
#' @inheritParams samplesim
#'
#' @return NULL
#' 
#' @seealso [samplesim()], [get_output()], [plot_samplesim()]
#' 
#' @export
#' @import ggplot2
#'
#' @examples
#' \dontrun{
#' ## Please visit the vignette available at: 
#' ## https://ahasverus.github.io/samplesim/articles/samplesim.html
#' }

plot_isospace <- function(mix, source, discr, filename = "isospace", 
                          plot_save_pdf = FALSE, plot_save_png = FALSE) {


  
  if (length(mix$"FAC") > 0 || length(source$"S_factor1") > 0) {
    stop("Your data contain at least one factor. ", 
         "Please use MixSIAR::plot_data() instead.")
  }


  spaces <- utils::combn(1:mix$"n.iso", 2)
  nplots <- ncol(spaces)

  for (i in 1:nplots) {

    iso_names <- mix$"iso_names"[spaces[ , i]]

    if (length(grep("C$", iso_names[1])) == 1) {

      x_label <- expression(paste(delta^13, "C (\u2030)", sep = ""))
    }

    if (length(grep("C$", iso_names[2])) == 1) {

      y_label <- expression(paste(delta^13, "C (\u2030)", sep = ""))
    }

    if (length(grep("N$", iso_names[1])) == 1) {

      x_label <- expression(paste(delta^15, "N (\u2030)", sep = ""))
    }

    if (length(grep("N$", iso_names[2])) == 1) {

      y_label <- expression(paste(delta^15, "N (\u2030)", sep = ""))
    }

    if (length(grep("S$", iso_names[1])) == 1) {
      x_label <- expression(paste(delta^34, "S (\u2030)", sep = ""))
    }

    if (length(grep("S$", iso_names[2])) == 1) {

      y_label <- expression(paste(delta^34, "S (\u2030)", sep = ""))
    }

    if (length(grep("O$", iso_names[1])) == 1) {

      x_label <- expression(paste(delta^18, "O (\u2030)", sep = ""))
    }

    if (length(grep("O$", iso_names[2])) == 1) {

      y_label <- expression(paste(delta^18, "O (\u2030)", sep = ""))
    }

    dat_mix <- data.frame(x = mix$"data_iso"[ , iso_names[1]],
                          y = mix$"data_iso"[ , iso_names[2]])

    mu  <- data.frame(rep(0, source$"n.sources"), rep(0, source$"n.sources"))
    colnames(mu) <- iso_names
    
    sig <- mu

    for (iso in iso_names) {
      
        mu[ , iso]  <- source$"S_MU"[ , paste0("Mean", iso)] + 
          discr$"mu"[ , paste0("Mean", iso)]
        
        sig[ , iso] <- sqrt(source$"S_SIG"[ , paste0("SD", iso)] ^ 2 +
                              discr$"sig2"[, paste0("SD", iso)])
    }

    dat_src <- data.frame("x"      = mu[ , 1], 
                          "y"      = mu[ , 2],
                          "xmin"   = mu[ , 1] - sig[ , 1],
                          "xmax"   = mu[ , 1] + sig[ , 1],
                          "ymin"   = mu[ , 2] - sig[ , 2],
                          "ymax"   = mu[ , 2] + sig[ , 2],
                          "source" = source$"source_names")

    if (i > 1) {
      grDevices::dev.new()
    }

    gg <- ggplot(data = dat_src, aes(x = x, y = y)) +
      
      geom_point(data = dat_mix, aes(x = x, y = y), colour = "#888888",
                 show.legend = TRUE) +
      
      geom_errorbar(data = dat_src, aes(ymin = ymin, ymax = ymax, 
                                        colour = source), width = 0) +
      
      geom_errorbarh(data = dat_src, aes(xmin = xmin, xmax = xmax, 
                                         colour = source), height = 0) +
      
      geom_point(data = dat_src, aes(x = x, y = y, colour = source), shape = 24,
                 fill = "white", size = 3) +
      
      labs(x = x_label, y = y_label) +
      
      theme_light() +
      theme(legend.position = "bottom", legend.title = element_blank())

    print(gg)

    if (plot_save_pdf) {

      grDevices::cairo_pdf(
        filename = paste0(filename, "-space", i, ".pdf"),
        width = 6, height = 6)
      
      print(gg)
      
      grDevices::dev.off()
    }

    if (plot_save_png) {

      grDevices::png(file = paste0(filename, "-space", i, ".png"))
      
      print(gg)
      
      grDevices::dev.off()
    }
  }
  
  invisible(NULL)
}