R/plotBio_InWat.r

In PDXChris/pmtools: Tools for Working with PAWMAP Data

#' Plot PAWMAP biological metrics within a selected watershed.
#'
#' @param dfm  The data frame containing the variable
#' @param vbl the field containing the metric to plot
#' @param wat the watershed to plot
#' @param bio type of biological data to plot.  Options: 'bugs', 'birds', 'fish'
#' @param ... Additional arguments to control aesthetic of plotted points (must be string)
#' @return A ggplot dot plot of the Macroinvertebrate Observed/Expected scores
#' within a watershed
#' @examples
#' library(ggplot2)
#' site_identifier <- unique(stationInfo$site_identifier[stationInfo$duration=='P'])
#' d <- data.frame(site_identifier=unique(site_identifier), metric_name='oep5',
#'                  watershed='Tryon Creek', result=rnorm(length(site_identifier)))
#' d <- mergeStatInfo(d)
#' p <- plotBio_InWat(d, 'result', 'Johnson Creek', 'bugs')
#' p + ggtitle('Macroinvertebrate Observed/Expected - Generated Data for Example\n')
#' @import ggplot2
#' @export

plotBio_InWat <- function(dfm, vbl, wat, bio = c('bugs', 'birds', 'fish'), ...) {

  bio <- match.arg(bio)

  # Limit to named watershed
  tmp <- dfm[dfm[['watershed']] == wat, ]

  # Sort data by mean of seasonal data
  tmp <- transform(tmp, loc.lbl=reorder(loc.lbl, tmp[, vbl]))

  ## Set generic plot
  p <- ggplot(data = tmp, aes_string('loc.lbl', vbl)) + xlab('') +
    coord_flip() + theme_bw() + theme(axis.text = element_text(size=14),
          title = element_text(size = rel(1.3)))

  if(length(list(...))) {
    p <- p + geom_point(size=4, aes_string(...))
    } else {p <- p + geom_point(size=4)}

  ## For Macroinvertebrate Observed/Expected
  if (bio=='bugs') {
    ttl <- paste0("Macroinvertebrate Observed/Expected Scores\nin ", wat, "\n")
    p <- p + geom_hline(yintercept=0.91, color='darkgreen', size=1.2) +
      geom_hline(yintercept=0.85, color='red', size=1.2) +
      ylab('\nObserved/Expected') +
      ggtitle(ttl)
  }

  ## For Bird Integrity Index
  if (bio=='birds') {
    ttl <- paste0('Bird Integrity Index in ', wat, '\n')
    p <- p + ggtitle(ttl) +
      ylab('\nBird Integrity Index Score')
  }

  ## For Fish Integrity Index
    if (bio=='fish') {
      ttl <- paste0('Fish Index of Biotic Integrity in ', wat, '\n')
      p <- p + geom_hline(yintercept=75, color='darkgreen', size=1.2) +
      geom_hline(yintercept=50, color='red', size=1.2) +
      ylab('\nFish Index of Biotic Integrity') +
      ggtitle(ttl)
  }


  return(p)

}