--- /dev/null
+# R script showing .pdf file with plots of all injection histograms for a certain file
+
+# Can be called from the command line with:
+# Rscript $this_script.R inputfile
+
+# Necessary libraries
+library(plyr)
+library(ggplot2)
+library(data.table)
+library(grid)
+
+# Functions for arranging multiple plots
+vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y)
+arrange_ggplot2 <- function(list, nrow=NULL, ncol=NULL, as.table=FALSE) {
+n <- length(list)
+if(is.null(nrow) & is.null(ncol)) { nrow = floor(n/2) ; ncol = ceiling(n/nrow)}
+if(is.null(nrow)) { nrow = ceiling(n/ncol)}
+if(is.null(ncol)) { ncol = ceiling(n/nrow)}
+## NOTE see n2mfrow in grDevices for possible alternative
+grid.newpage()
+pushViewport(viewport(layout=grid.layout(nrow,ncol) ) )
+ii.p <- 1
+for(ii.row in seq(1, nrow)){
+ii.table.row <- ii.row
+if(as.table) {ii.table.row <- nrow - ii.table.row + 1}
+for(ii.col in seq(1, ncol)){
+ii.table <- ii.p
+if(ii.p > n) break
+print(list[[ii.table]], vp=vp.layout(ii.table.row, ii.col))
+ii.p <- ii.p + 1
+}
+}
+}
+
+### Main
+
+# Reading command line argument with the input file path
+args <- commandArgs(trailingOnly = TRUE)
+fp <- file(args[1], open = "r")
+
+plots<-list()
+i<-1
+
+# Reading histograms one by one, line by line
+while (length(oneLine <- readLines(fp, n = 1, warn = FALSE)) > 0)
+{ myVector <- (strsplit(oneLine, "\t"))
+
+ dfl <- ldply (myVector, data.frame)
+
+ name<-as.character(dfl[1,])
+ nbins<-as.numeric(as.character(dfl[4,]))
+ allbreaks<-as.numeric(as.character(dfl[5:(5+nbins-1),]))
+
+ dh<-data.frame(Name=as.character(dfl[1,]), Total=as.numeric(as.character(dfl[2,])), Mean=as.numeric(as.character(dfl[3,])), Nbins=as.numeric(as.character(dfl[4,])))
+ dh<-cbind(dh,Bstart=allbreaks[-length(allbreaks)])
+ dh<-cbind(dh,Bend=allbreaks[-1])
+ dh<-cbind(dh,Density=as.numeric(as.character(dfl[(5+nbins):(5+nbins*2-2),])))
+
+ # Plotting single histogram, if it only has one value then use geom_bar
+ if (nbins > 2)
+ plots[[i]]<-ggplot(data=data.frame(dh), aes(xmin=Bstart, xmax=Bend, ymin=0, ymax=Density)) + geom_rect(aes(fill=Density)) + theme_bw() + scale_x_continuous("Time [s]", allbreaks) + labs(title=name, y=element_text("Density %"))
+ else
+ plots[[i]]<-ggplot(data=data.frame(dh), aes(factor(Bstart))) + geom_bar(aes(fill=Density)) + theme_bw() + labs(title=name, y=element_text("Density %"), x=element_text("Time [s]"))
+
+ i<-i+1
+}
+
+# Printing all plots together in a table
+arrange_ggplot2(plots, as.table=TRUE)
+
+# End
+write("Done producing a histogram plot. Open Rplots.pdf located in this folder to see the results", stdout())
