R/mcs_plo.R

In SCCWRP/SQObioaccumulation: Run bioaccumulation model for SQO human health objectives

#' Create MCS summary plot
#'
#' @param mcsres output from \code{\link{mcs_fun}}
#' @param alpha numeric value for transparency of background fill
#' @param xmax numeric value for upper limit of x-axis, defaults to 95th percentile of all linkage values
#'
#' @export
#'
#' @import ggplot2 shadowtext
mcs_plo <- function(mcsres, alpha = 0.4, xmax = NULL){

  # input
  toplo <- mcsres 
  if(is.null(xmax))
    xmax <- quantile(toplo$sitsedlnk, 0.95, na.rm = TRUE)[[1]]

  rctcols <- c('tomato1', 'lightgoldenrod1', 'lightyellow', 'lightgreen')
  
  # plot
  p <- toplo %>%
    ggplot() +
    scale_x_continuous(expand = c(0, 0)) + 
    scale_y_continuous(expand = c(0, 0)) +
    annotate("rect", xmin = 0, xmax = xmax, ymin = 0,    ymax = 0.25, alpha = alpha, fill = rctcols[1]) +
    annotate("rect", xmin = 0, xmax = xmax, ymin = 0.25, ymax = 0.5,  alpha = alpha, fill = rctcols[2]) +
    annotate("rect", xmin = 0, xmax = xmax, ymin = 0.5,  ymax = 0.75, alpha = alpha, fill = rctcols[3]) +
    annotate("rect", xmin = 0, xmax = xmax, ymin = 0.75, ymax = 1,    alpha = alpha, fill = rctcols[4]) +
    stat_ecdf(aes(sitsedlnk, linetype = contam),
              geom = "line", size = 1.25) +
    geom_vline(xintercept = 0.5, lty = "dashed", color = "blue") +
    geom_shadowtext(aes(x = xmax - (0.1 * xmax), y = .125, label = "High"), size = 6, colour = rctcols[1], check_overlap = T) +
    geom_shadowtext(aes(x = xmax - (0.1 * xmax), y = .375, label = "Moderate"), size = 6, colour = rctcols[2], check_overlap = T) +
    geom_shadowtext(aes(x = xmax - (0.1 * xmax), y = .615, label = "Low"), size = 6, colour = rctcols[3], check_overlap = T) +
    geom_shadowtext(aes(x = xmax - (0.1 * xmax), y = .875, label = "Very Low"), size = 6, colour = rctcols[4], check_overlap = T) +
    labs(x = 'Site Linkage Factor',
         y = 'Cumulative Proportion',
         title = 'Site Linkage',
         fill = '') +
    # scale_colour_manual(values = c('darkblue', 'darkred', 'darkgreen', 'purple')) +
    scale_linetype_manual(values = c('solid', 'dashed', 'dotted', 'dotdash')) +
    theme_bw(base_family = 'serif', base_size = 16) +
    theme(
      legend.position="top", 
      legend.title = element_blank(), 
      legend.text = element_text(size = 14),
      legend.key.width = unit(2.5,"cm")
      ) + 
    coord_cartesian(xlim = c(0, xmax), ylim = c(0, 1))

  return(p)
  
}