R/plot_fish_backscatter_data.R

In tessington/pelagichypoxia: Bayesian analysis of food web responses to low dissolved oxygen

#' plot_fish_backscatter_data
#'@description
#' creates a plot showing the estimated backscatter for Pacific Hake and Pacific Herring
#' By month, sample site, and year.
#'
#'
#' @return
#' stores a pdf file "fish_sa" in graphics folder
#'
#'
#'
#' @export
#'
#' @examples
#'

plot_fish_backscatter_data<- function(){
require(viridis)
col <- plasma(n=16)[c(1,6,11,16)]

cur.dir <- dir()
if (!"graphics" %in% cur.dir) dir.create("graphics")

thehakedata <- load_sa_fish_data("Pacific Hake")
theherringdata <- load_sa_fish_data("Pacific Herring")


# so now a plot with month on the x axis, log (NASC)on the y axis, and a point for each site

ylim <- c(1,9)
sites <- c("A","B","C","D")
site.labels <- c("Union",
                 "Hoodsport",
                 "Duckabush",
                 "Dabob Bay")
months <- c("Jun","Jul","Aug","Sep","Oct")

years = c(2012, 2013)
plot.labels <- c("2012 Herring", "2013 Herring", "2012 Hake", "2013 Hake")

plotfilename <- "graphics/fish_sa.pdf"
pdf(file = plotfilename, height = 7.5, width = 8)
layout.mat <- matrix(c(1,1,2,2,1,1,2,2,3,3,4,4,3,3,4,4), byrow = T, ncol = 4, nrow = 4)
layout(mat = layout.mat)
species.list <- c("herring","hake")
par(oma = c(0.5,.5, 0.5, 0.5), mar = c(5,5,0,0))
for (sp in 1:2){

  eval( parse(text = paste("plotdata <- the",species.list[sp],"data", sep = "")))

  for (j in 1:2) {

    # cycle through each site an plot (one year at a time)

    plot(c(),c(),
         type = "n",
         las = 1,
         xlim = c(1,5),
         ylim = ylim,
         xlab = "",
         ylab = "",
         axes = F)
    box()
    if (sp ==2) axis(side = 1, at = 1:5, labels = months, cex.axis = 1.5)
    axis(side = 2, las = 1, cex.axis = 1.5)
    ### now plot sz

    for (i in 1:length(sites)) {
      plot.data <- plotdata %>%
        filter(Year == years[j], Site == sites[i])

      points(plot.data$Month, (plot.data$y), pch = 21, bg = col[i], cex = 2.5)
    }
    if (j == 1) mtext(expression(paste("log NASC (m"^"2","nmi"^"-2",")", sep = "")), side = 2, line =3, las = 0)
    if (sp ==1) text(plot.labels[j], x= 1 , y = 8.5, pos = 4, cex = 1.5)
    if (sp == 2) text(plot.labels[j+2], x= 1 , y = 8.5, pos = 4, cex = 1.5)
  }
}
dev.off()
}