R/plotRaw.R

In diskImageR: A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

#' Used to plot the results of the imageJ analysis

#' @description \code{plotRaw} creates a pdf figure showing the results of the ImageJ analysis, with one plot for each photograph. This function is optional, and is primarily for visualization purposes.

#' @param projectName the short name to be used for the project
#' @param ymin a numeric value indicating the minimum y value plotted in each plot
#' @param ymax a numeric value indicating the maximum y value plotted in each plot
#' @param xmin a numeric value indicating the minimum x value plotted in each plot
#' @param xmax a numeric value indicating the maximum x value plotted in each plot
#' @param xplots a numeric value indicating how many plots to plot in each row
#' @param height a numeric value indicating the height of the pdf file generated
#' @param width a numeric value indicating the width of the pdf file generated
#' @param cexPt a numeric value indicating the size to plot for points
#' @param cexX a numeric value indicating the size of x-axis text
#' @param cexY a numeric value indicating the size of y-axis text
#' @param nameVector either a logial value indicating whether to plot the photograph names above the plot; a vector the same length as the number of photographs containing the desired names. Defaults to TRUE.
#' @param standardLoc a numberic value indicating the location (on the disk) to use to standardize intensity across photographs. The position of standardLoc is a position that should theoretically have the same intensity in all photographs, i.e., the white of the disk. The defaul value (2.5mm) was chosen after testing of 6mm disks that contain some writing. If smaller disks are used standardLoc should be scaled appropriately. 
#' @param plotStandardLoc a logical value indicating whether to draw a dashed vertical line at the standardization point that is used in \code{maxLik} and \code{createDataframe}

#' @param showNum a logical value indicating whether to annotate each plot with the photograph number (determined alphabetically from the photograph names). This can be helpful for later functions that require the numerical place of a photograph with a clear halo.
#' @param popUp a logical value indicating whether to pop up the figure after it has been created
#' @param overwrite a logical value indicating whether to overwrite existing figures created on the same day for the same project name
#' @param savePDF a logical value indicating whether to save a PDF file or open a new quartz window. Defaults to TRUE (saves a pdf file).

#' @return A pdf file with one plot for each photograph is saved to visualize the results of imageJ analyses

#' @examples 
#' \dontrun{
#' plotRaw("myProject")
#' plotRaw("myProject", ymin = 50, ymax = 300, xplots=2, height=3, width=4, plotStandardLoc=FALSE)
#' }

#' @export

plotRaw <- function(projectName, ymin = 0, ymax=250, xmin = 0, xmax = 40, xplots = 6, height =4, width = 8, cexPt = 0.6, cexX = 0.8, cexY = 0.8, standardLoc = 2.5, nameVector = TRUE , plotStandardLoc=TRUE, showNum=FALSE, popUp = TRUE, overwrite=TRUE, savePDF= TRUE){
	dir.create(paste("figures/", projectName,  sep=""), showWarnings = FALSE)
	t <- file.path("figures", projectName,  paste(projectName, "_raw.pdf", sep=""))
	if (!overwrite){
		if (file.exists(t)){
			t <- file.path("figures", projectName, paste(projectName, "_raw_2.pdf", sep=""))
			if (file.exists(t)){
				k <- 2
				while(file.exists(t)){
					k <- k+1
					t <- file.path("figures", projectName, paste(projectName, "_raw_", k, ".pdf", sep=""))
					}
				}
			}
		}
	data <- eval(parse(text=projectName))
	dotMax <- max(sapply(data, function(x) {x[which(x[,1] > standardLoc)[1], 2]})) 		
	standards <-c( sapply(data, function(x) {dotMax-x[which(x[,1] > standardLoc)[1], 2]}))	
	convert <- unlist(lapply(data, function(x) 40/length(x[,1])))
	if (is.logical(nameVector)){
		if (nameVector){label <- names(data)}		
		else {label <- rep("", length(data))}
		}
	else {label <- nameVector}

	if (xplots > length(data)){
		xplots <- length(data)
		}
	if (ceiling(length(data)/xplots) < 6) {
		yplots<- ceiling(length(data)/xplots)}
	else {yplots<- 6}
	numpages <- ceiling(length(data)/(xplots*yplots))
	if(savePDF){
		pdf(t, width=width, height=height)
		}
	# if(!savePDF){
		# quartz(width=width, height=height)
		# }
	par(mfrow=c(yplots , xplots), mar=c(1,1,1,1), oma=c(4,5,1,1))
	for (i in 1:length(data)){
		.discplotNoRep(data[[i]], label[i], ymin=ymin, ymax=ymax, xmin=xmin, xmax=xmax, stand=standards[i], standardLoc = standardLoc, cexPt = cexPt, plotStandardLoc = plotStandardLoc)
		if(numpages == 1){
			if (i >= xplots*yplots-xplots+1){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
		}
		if(numpages == 2){
			if (i >= xplots*yplots-xplots+1 & i < xplots*yplots+1){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
			if (i >= 2*xplots*yplots-xplots+1){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
		}				
		if(numpages == 3){
			if (i >= xplots*yplots-xplots+1 & i < xplots*yplots+1){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
			if (i >= 2*xplots*yplots-xplots+1 & i < 2*xplots*yplots+1){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
			if (i >= (length(data)-xplots)){
				axis(1, cex.axis=cexX, at=c(0, 10, 20, 30, 40), labels=c(0, 10, 20, 30, 40))
			}
		}				
		k <- 1
		while (k <= numpages){
		if (i %in% seq(1, k*yplots*xplots, by=xplots)) {axis(2, cex.axis=cexY, las=2)}
			k <- k+1}
		if(showNum){
			text(xmax*0.95, xmax*0.95, i)
		}
	}
	mtext("Distance from center of disk (mm)", side= 1, outer=TRUE, line=2)
	mtext("Pixel intensity", side=2, outer=TRUE, line=2)
	if(savePDF){
		dev.off()
		cat(paste("\tFigure saved: ", t, sep=""))
		if(popUp){
		tt <- paste("open ",t)
		system(tt)
	}
	}
	}

.discplotNoRep <- function(data,  label=label, ymin=0, ymax=250, xmin=0, xmax=40, standardLoc = 2.5, cexPt = 0.6, stand = 0, xaxt="n", yaxt="n", plotStandardLoc =FALSE){
	plot(data[,1], data[,2]+stand, ylim=c(ymin, ymax), xlim=c(xmin, xmax), xaxt=xaxt, yaxt="n", cex=cexPt, col="black")
	if (yaxt=="s"){
		axis(2, las=2)}
	axis(1, labels=FALSE, at=c(0, 10, 20, 30, 40))
	axis(2, labels=FALSE)
	mtext(label, side=3, cex=0.6)
	if(plotStandardLoc){
		abline(v= standardLoc, lty=2, col="red")
		}
	}