plot.abline <-
function(
	intercept = 0,
	slope = 1,
	black.and.white = black.and.white.in.panel
){
	cat("\nPlotting abline (",intercept,",",slope,")\n")
	
	if(black.and.white){
		line.color = "black"
		line.style = "dotted"
		line.thickness = 2
	}else{		
		line.color = "darkblue"
		line.style = "dotted"
		line.thickness = 2
	}

	panel.abline(
		a = intercept,
		b = slope,
		col = line.color,
		lwd = line.thickness,
		lty = line.style
	)
}


plot.administration.time.multi <-
function(
	data.for.amt = data.to.plot.in.panel,
	ids = groups,
	rows.being.used = subscripts,
	black.and.white = black.and.white.in.panel
){

	unique.ids <- unique(ids[rows.being.used])
	amt.data <- data.for.amt[["amt"]]

#cat("\n\nAMT Data\n");print(amt.data)
	
	amt.data.select <- c(amt.data[amt.data[,"ID"] %in% unique.ids,"TIME"] )
		#To select the administration times where the IDs are being plotted
	
#cat("\n\nSelected AMT Data\n");print(amt.data.select)
	
	if(black.and.white){
		polygon.color = "grey50" #medium grey
		amt.color = "grey5" #almost black
	}else{
		polygon.color = "green"
		amt.color = "green"
	}

	if(length(amt.data.select) > 0){
		cat("\nPlotting Administration time\n")

		panel.abline(v = unique(amt.data.select),col = amt.color)
			#Plot the unique times
			
	}else{
		cat("\n There is no AMT times being used. AMT lines will not appear. \n")
	}
}
	

plot.administration.time <-
function(
	data.for.amt = data.to.plot.in.panel,
	ids = groups,
	rows.being.used = subscripts,
	black.and.white = black.and.white.in.panel
){

	unique.ids <- unique(ids[rows.being.used])
	amt.data <- data.for.amt[["amt"]]

#cat("\n\nAMT Data\n");print(amt.data)
	
	amt.data.select <- c(amt.data[amt.data[,"ID"] %in% unique.ids,"TIME"] )
		#To select the administration times where the IDs are being plotted
	
#cat("\n\nSelected AMT Data\n");print(amt.data.select)
	
	if(black.and.white){
		polygon.color = "grey50" #medium grey
		amt.color = "grey5" #almost black
	}else{
		polygon.color = "green"
		amt.color = "green"
	}

	if(length(amt.data.select) > 0){
		cat("\nPlotting Administration time\n")

		amt.range <- range(amt.data.select) 

		if(amt.range[1] == amt.range[2]){
			panel.abline(v = amt.range[1],col = amt.color)
		}else{
			polygon.points <- rbind(
				c(amt.range[1],y.min.lim),
				c(amt.range[2],y.min.lim),
				c(amt.range[2],y.max.lim),
				c(amt.range[1],y.max.lim)
			)
			panel.polygon(polygon.points,col = polygon.color,border = polygon.color)
		}
			
	}else{
		cat("\n There is no AMT times being used. AMT lines will not appear. \n")
	}
}


plot.box.and.whiskers <-
function(
	points.x = x,
	points.y = y,
	minimum.required = 6,
	black.and.white = black.and.white.in.panel
){
cat("\nPlotting Box and Whiskers\n")
	### Box Plot Box Color (Default color is blue)
	box.rectangle <- trellis.par.get("box.rectangle")
	box.rectangle$col <- "black"
	trellis.par.set("box.rectangle", box.rectangle)

	### Box Plot Outliers
	outlier.color <- "black"
	plot.symbol <- trellis.par.get("plot.symbol")
	plot.symbol$col <- outlier.color
	plot.symbol$cex <- 1
	trellis.par.set("plot.symbol", plot.symbol)

	### Box Plot Whiskers
	whisker.color <- "black"
	box.umbrella <- trellis.par.get("box.umbrella")
	box.umbrella$col <- whisker.color
	trellis.par.set("box.umbrella", box.umbrella)


	if(black.and.white){
		boxfill.color <- "grey 90"
	}else{
		boxfill.color <- "light yellow"
	}
		
	table.points.x <- table(points.x)
	locations.x <- table.points.x[table.points.x >= minimum.required]
	x.names <- as.numeric(names(locations.x))

	if(length(x.names) > 0){
		x.box.points <- points.x[points.x %in% x.names]
		y.box.points <- points.y[points.x %in% x.names]
			### Select only locations that contained the minimum requirement

#cat("Table of X.Points\n");print(table.points.x)
#cat("X Points that Passed");print(x.names)
#cat("x.box.points");print(x.box.points)
#cat("y.box.points");print(y.box.points)

		panel.bwplot(
			x = x.box.points,
			y = y.box.points,
			horizontal = FALSE,
			color = "black",	### Color of "dot at median"
			pch="|",	### Creates a horizontal line at the median, instead of a solid dot
			fill = boxfill.color
		)
	}else{
		cat("\nWarning!\n\tPlease lower the minimum required for the box and whisker plot to allow boxes to be plotted.\n\t(Only if desired)\n")
	}
}


plot.grid <-
function(
	x.divisions = 10,
	y.divisions = 10,
	grid.color = "grey95",	### Really close to white
	x.limits = data.to.plot.in.panel[["x.lim"]],
	y.limits = data.to.plot.in.panel[["y.lim"]]
){
cat("\nPlotting Grid\n")

	tmp.h <- (0:y.divisions)/y.divisions *(diff(y.limits)) + y.limits[1] 
	tmp.v <- (0:x.divisions)/x.divisions *(diff(x.limits)) + x.limits[1]

	panel.abline(h = tmp.h,v = tmp.v,col = "grey95")
}	
	
	
plot.grid.simple <- 
function(
	x.divisions = 10,
	y.divisions = 10,
	grid.color = "grey95"	### Really close to white
){
cat("\nPlotting Simple Grid\n")
	
	panel.grid(
		h = y.divisions,
		v = x.divisions,
		col = grid.color
	)
}


lines.by.id <-
function(
	points.x = x,
	points.y = y,
	ids = groups,
	rows.being.plotted = subscripts,
	black.and.white = black.and.white.in.panel
){
cat("\nPlotting Lines Connected by ID\n")

	unique.ids <- unique(ids)

	if(black.and.white){ 
		colors.unique <- c(rep(1,length(unique.ids) ))
		line.style <- "dashed"
	}else{
		colors.unique <- rainbow( length(unique.ids) ,start = .56,end = .13)
			#Colors blue to purple to red to orange, no yellow and green
		line.style <- "solid"
	}
	
  panel.superpose(
    x = points.x,
    y = points.y,
    subscripts = rows.being.plotted,
    groups = ids,
    panel.groups = "panel.lines", # Panel used to plot the data
    col = colors.unique,
    pch = NA,
    lty = line.style,
    type = "l",
    alpha = 1  # The opacity of the lines
  )
}


plot.lowess <-
function(
	points.x = x,
	points.y = y,
	line.thickness = 1.4,
	line.style = "solid",
	line.color = "black",
	line.span = 5/6
){
cat("\nPlotting Loess Line\n")

	if(length(points.x) > 1){
		panel.loess(
			x = points.x,
			y = points.y,
			lwd = line.thickness,
			lty = line.style,
			col = line.color,
			span = line.span
		)
	}else{
		cat("\nNot enough points to plot a Loess line\n")
	}
}


plot.mean.line <-
function(
	points.x = x,
	points.y = y,
	line.style = "dotted",
	minimum.required = 2,
	black.and.white = black.and.white.in.panel
){
	cat("\nPlotting Mean Line\n")
	
	if(black.and.white){
		line.color <- "black"
		line.thickness <- 2
	}else{
		line.color <- "darkred"
		line.thickness <- 2
	}
	
	
	table.points.x <- table(points.x)
	unique.ordered.points.x <- names(table.points.x[table.points.x >= minimum.required])
#cat("\ntable.points.x\n");print(table.points.x >= minimum.required)
#cat("\nunique.ordered.points.x\n");print(unique.ordered.points.x)

	avg.y.points <- sapply(unique.ordered.points.x,function(x,s.points.y = points.y, s.points.x = points.x){
		s.points.mean <- mean( s.points.y[s.points.x %in% x] )
		return(s.points.mean)
	})
	
#cat("\navg.y.points\n");print(avg.y.points)
	if(length(unique.ordered.points.x > 0)){
		panel.lines(x = unique.ordered.points.x, y = avg.y.points, lwd = line.thickness, lty = line.style, col = line.color)
	}else{
		cat("\nWarning!\n\tPlease lower the minimum required for the mean line to allow the line to be plotted.\n\t(Only if desired)\n")
	}
}


plot.points <- 
function( 
	points.x = x, 
	points.y = y, 
	points.symbol = "x", 
	points.size = 1, 
	points.color = "black"
){
cat("\nPlotting Points\n")

	panel.xyplot(
		x = points.x,
		y = points.y,
		pch = points.symbol,
		cex = points.size,
		col = points.color
	)
}


plot.quantiles <- 
function(
	quantile.data = quantiles.to.plot.in.panel,
	quantile.type = 7
){
cat("\nPlotting Quantiles\n")

	quan.x <- quantile.data$x
	quan.y <- quantile.data$y
	quan.alpha <- quantile.data$alpha
		
	fifty.percent.line <- tapply(quan.y, quan.x, quantile, probs = 0.5, type = quantile.type)
	nintyfive.percent.line <- tapply(quan.y, quan.x, quantile, probs = (1-quan.alpha), type = quantile.type)
	five.percent.line <- tapply(quan.y, quan.x, quantile, probs = (quan.alpha), type = quantile.type)

#cat("\n\n50% Line\n");print(fifty.percent.line)

		quantile.colors <- c("grey35","grey35")
		quantile.lty <- c("dashed","longdash")

	panel.lines(names(five.percent.line),(five.percent.line), col=quantile.colors[1],lty=quantile.lty[1],lwd=2)
	panel.lines(names(fifty.percent.line),(fifty.percent.line), col=quantile.colors[2],lty=quantile.lty[2],lwd=2)
	panel.lines(names(nintyfive.percent.line),(nintyfive.percent.line), col=quantile.colors[1],lty=quantile.lty[1],lwd=2)

}

'plot.violin' <-
function(
  points.x = x,
  points.y = y,
  cut.off = 0,
  violin.color = "transparent",
  violin.ghost = .5
){
cat("\nPlotting Violin Plot\n")

  ### Violin Color and Alpha (Default color is blue; Default alpha is 1)
  viol <- trellis.par.get("plot.polygon")
  viol$col <- violin.color
  viol$alpha <- violin.ghost
  trellis.par.set("plot.polygon", viol)
    
  panel.violin(
    x = points.x,
    y = points.y,
    horizontal = FALSE,
    cut=cut.off
  )
}

'plot.ci95.whisker' <- 
function(
  points.x = x, 
  points.y = y, 
  distribution = "t", #"normal"
  y.limits = NULL,
  ci95.ghost = 1,
  whiskers.and.outliers = FALSE
){
cat("\nPlotting 95% Confidence Interval\n")
  
  if(is.null(y.limits)) stop("\n\n\ty.limits was not supplied\n\n")

  y.split <- split(points.y,points.x)
  x.locations <- as.numeric(names(y.split))

  for( i in x.locations){
    x <- i    
    y <- y.split[[as.character(x)]]
    a <- mean(y)
    s <- sd(y)
    n <- length(y)
    if(distribution == "t") error <- qt(0.975,df=n-1)*s/sqrt(n)
    if(distribution == "normal") error <- qnorm(0.975)*s/sqrt(n)
    
    top.ci <- a + error
    bot.ci <- a - error

    ### Plot Lower Interval
    lsegments(
      x0 = x,  # X Start
      y0 = bot.ci,  #Y Start
      x1 = x,  # X Finish
      y1 = min(a,c(a - 0.02*diff(y.limits))),  # Y Finish, with 2% buffer away from center point (creates white space)
      col = "black",
      lty = 1,
      lwd = 8,
      alpha = .25
    )
    
    ### Plot Upper Interval
    lsegments(
      x0 = x,
      y0 = top.ci,
      x1 = x,
      y1 = max(a,c(a + 0.02*diff(y.limits))),
      col = "black",
      lty = 1,
      lwd = 8,
      alpha = .25
    )
    
    ### Plot Mean Dot
    lpoints(
      x = x, 
      y = a,
      pch = 16, # Solid Circle
      col = "black",
      cex = .75,
      alpha = ci95.ghost
    )

    ### Write how many points there are at the bottom
    ltext(
      x = x,
      y = c(y.limits[1]-diff(y.limits)*0),  # To have the text written in the 3% buffer
      offset = 0,
      labels = c(paste("N =",n,sep=" ",collapse="")),
      cex = .5,
      srt = 90,  # Rotate text 90 degrees
    )

    
    ### Make Box Plot Box Color Transparent
    box.rectangle <- trellis.par.get("box.rectangle")
    box.rectangle$col <- "transparent"
    trellis.par.set("box.rectangle", box.rectangle)

    ### Make Box Plot Outliers Circles
    outlier.color <- "black"
    plot.symbol <- trellis.par.get("plot.symbol")
    plot.symbol$col <- outlier.color
    plot.symbol$cex <- 1
    trellis.par.set("plot.symbol", plot.symbol)

    ### Make Box Plot Whiskers Black, Solid, and See Through
    whisker.color <- "black"
    box.umbrella <- trellis.par.get("box.umbrella")
    box.umbrella$alpha <- ci95.ghost
    box.umbrella$col <- whisker.color
    box.umbrella$lty <- "solid"
    trellis.par.set("box.umbrella", box.umbrella)

    ### Make Whiskers and Outliers
    if(whiskers.and.outliers){
      panel.bwplot(
        x = rep(x,length(y)),
        y = y,
        horizontal = FALSE,
        color = "white",  ### Best way known how to remove the dot
        pch=".", ### Best way known how to remove the dot
        cex = 0.000001, ### Best way known how to remove the dot
        fill = "transparent",  # Makes box see-through
        box.width = 0 # Makes whisker top line disappear
      )
    }

#cat("\n\n\nX");print(x);cat("a");print(a);cat("s");print(s);cat("n");print(n);cat("error");print(error);cat("top.ci");print(top.ci);cat("bot.ci");print(bot.ci);cat("diff");print(0.02*diff(y.limits))

  }
  
}