Swiss Interaction.Plots_fun.R

# define the function:
Interaction.Plots_fun <- function(MyMatrix.lst, data.lst) {
  # storing default par() for reverting par to original/default values
  par.default <- par()
  # on.exit(par(par.default)) # when exiting function par(), restore to default (? - need to test!)
  # par(par.default) # or simply call each time this line
  
  # open a pdf device with desired parameters
  pdf(file=paste0("Mueller ", format(Sys.time(), "%Y-%m-%d %H-%M-%p"), ".pdf"), onefile=TRUE, width=24, height=8.27)
  # remember that an A4 is 8.27 × 11.69 in. Here you want a landscape format width > height!
  # the width and height of the graphics region are in inches. The default values are 7.
  # to fit the grphs one must adjust the width and height; width=24, height=8.27 fits all graphs at all locations
  # format(Sys.time(), "%Y-%m-%d %H-%M-%p") # adds the time like: "2016-06-16 08-42-AM" # !! avoid special characters in the name of the file (e.g ":")
  my.cex <- 1 # store a universal value for the character expansion factor (default=1) [for adjusting text size in mtext()]
  # run for each matrix in MyMatrix.lst (that is, for each location)
  for (i in seq_along(MyMatrix.lst)) {
    # try to cath possible errors
    possibleError <- tryCatch({
      # __ plot interaction web __ #
      # par(mar=par.default$mar-2.5) # bipartite plot functions don't react to margins mar() options !!!
      bipartite::plotweb(MyMatrix.lst[[i]], arrow="down", 
                         labsize=1, text.rot=90, y.width.low=0.01, y.width.high=0.01, high.y=1.2, low.y=0.9)
      # display text to inform about the location
      mtext(paste0("Interaction network at location: ", i, " - ", names(MyMatrix.lst[i]), "; Altitude (range of means): ", 
                   paste0(range(as.numeric(data.lst[[i]]$altitude_mean)), "m", collapse=" - ")), 
            side=3, outer=T, line=-2, cex=my.cex)
      # __ plot interaction matrix __ #
      # this function has a horrible adjustment of labels! 
      bipartite::visweb(MyMatrix.lst[[i]], type="nested", labsize=0.5)
      # display text to inform about the location
      mtext(paste0("Interaction matrix at location: ", i, " - ", names(MyMatrix.lst[i]), "; Altitude (range of means): ", 
                   paste(range(as.numeric(data.lst[[i]]$altitude_mean)), "m", collapse=" - ")), 
            side=3, outer=T, line=-1, cex=my.cex)
      # __ plot altitude frequnecy table and isect order details __ #
      par(par.default) # this is needed because bipartite::visweb is distorting par parameters somehow without warnings! took me a while to figure this out :)
      par(mfrow = c(2,2)) # split the screen in 4
      # compute altitude frequnecy table
      alt.freq <- table(data.lst[[i]]$altitude_range, dnn = "Altitude classes and their frequencies:")
      # dnn - the names to be given to the dimensions in the result (just a trick to get some text above the table)
      # plot histogram of altitudes on first (up-left) screen with plot() - it works because alt.freq si a frequency table; can as well skip type = "h"
      plot(alt.freq, type = "h", lwd=5, frame.plot=FALSE, main="Altitude classess - histogram") 
      # plot histogram of insect order on the up-right screen
      plot(table(data.lst[[i]]$InsectOrderNew_WD), lwd=5, frame.plot=FALSE, 
           xlab="InsectOrderNew_WD", ylab="Freq", main="Insect order - histogram")
      # plot the content of the altitude frequnecy table on the down-left
      textplot(capture.output(alt.freq), cex=1.5, valign="top")
      par(par.default) # return par to default values (par.default was saved previosly)
      # display text to inform about the location (on top of the page)
      mtext(paste0("Details at location: ", i, " - ", names(MyMatrix.lst[i])), side=3, outer=T, line=-1, cex=my.cex)
    }, error=function(e) e)
    # in case of inheriting an error event:
    if(inherits(possibleError, "error")){
      frame() # plot empty graph
      # display text to inform about the error
      mtext(paste0("Plotting error for location: ", i, " - ", names(MyMatrix.lst[i]), ", due to small matrix dimensions"), side=3, outer=T, line=-2, cex=my.cex)
      mtext(paste0("number of rows in matrix: ", dim(MyMatrix.lst[[i]])[1]), side=3, outer=T, line=-5, cex=my.cex)
      mtext(paste0("number of columns in matrix: ", dim(MyMatrix.lst[[i]])[2]), side=3, outer=T, line=-7, cex=my.cex)
      next
    }
  }
  dev.off() # close the pdf device
  warnings() # show any wornings
}