< and you can download the pdf here
I found it a useful exercise - so I walk through the code below, but here are the source documents that I worked with for reference:
And here is the source data file which I had already transformed.
OK - here's the script. I've tried to put in as much commenting as possible to go through my thought process:
## required libraries require(ggplot2) require(grid) require(reshape2) ## load file from the working directory into new data frame OMEGAS tfile<-"OmegaTable.txt" OMEGAS<-read.table(tfile,header=TRUE,sep="\t",fill=TRUE) ## set various variables for the process strSearch<-"" # regexp expression for filtering the list maxRows<-30 # number of rows in the table ratioLimit<-15 # limits the max/min O3:6 ratio to display # this is to make the visual scale work: anything over 15 is just "high" # rather than overscaling xLabelLength<-40 # the label length for the items pngCover<-"Cover.png" # name of the cover image in the wd [I made this A4 ratio to help fit the doc] px=11.692 # page width (a4) py=8.267 # page height (a4) ## filter data OMEGAS<- OMEGAS[grep(strSearch, OMEGAS$EngName),] ## calculate the number of pages in the subset numPages<-floor(nrow(OMEGAS)/maxRows)+1 ## function to scale ratios for charting scaleRatio<-function(xR,xMax) { xScaled<-ifelse(xR >= 1,xR,-1/xR) # change the sub-1 fractions to ratio numbers return (pmin(xMax,pmax(xScaled,-xMax))) # apply the ratio limits } ## Update OmegaRatios so that ratios less than 1 are reflected as their negative inverse OMEGAS$OmegaRatio<-scaleRatio(OMEGAS$OmegaRatio,15) OMEGAS<- OMEGAS[order(-OMEGAS$OmegaRatio),] ## create placeholder frame for common rows which are applied to each page ## in order to add scale and ensure common scales for each plot ## these put a max and min bar on the graph so that ggplot scales each page the same placeRows<-c(" ",0,0,"",0, "_UPPER LIMIT 15:1 W3-W6 RATIO",0,0,"",ratioLimit+0.001, "_LOWER LIMIT 1:15 W3-W6 RATIO",0,0,"",-ratioLimit-0.001) placeRows<-data.frame(matrix(placeRows,nrow=(3),byrow=TRUE)) colnames(placeRows)<-colnames(OMEGAS) ## function to write the title page as a graph Put in the title page makeCover<-function(strPNG) { imgCover<-readPNG(strPNG) # set the image # create a blank plot, and make the dimensions a4 proportion plot(px/2, py/2,xlim=c(0,px),ylim=c(0,py), xaxt='n', yaxt='n', ann=FALSE) # write the PNG file on the graph using raster images rasterImage(imgCover,xleft=2,ybottom=0,xright=px,ytop=py) } ################# ## here I call the pdf device ################# # this gives the filename a unique suffix each time the script is run pdf(gsub("([: ])",replacement="",paste("OMEGAS",date(),".pdf")), px, py) ## Make the Cover by calling the function - this prints the cover to the first page makeCover(pngCover) ## run through the table in page-blocks of the size defined earlier for (pg in 1:numPages) { # subset the rows out of the main OMEGAS table for the page plotOMEGAS<-OMEGAS[(1+(maxRows*(pg-1))):(min((pg*maxRows),nrow(OMEGAS))),] # bind in the scaling rows plotOMEGAS<-data.frame(rbind(plotOMEGAS,placeRows)) # trim the x labels to size plotOMEGAS$EngName <- substr(plotOMEGAS$EngName,1,xLabelLength) # force the Ratio and Total columns to numeric and sort them plotOMEGAS$OmegaTotal<-as.numeric(plotOMEGAS$OmegaTotal) plotOMEGAS$OmegaRatio<-as.numeric(plotOMEGAS$OmegaRatio) plotOMEGAS <- transform(plotOMEGAS, EngName=reorder(EngName, OmegaRatio) ) bufferRows<-maxRows-nrow(plotOMEGAS) # check if the page requires "buffer" rows to keep the scale correct, if so, add them to the plot dataframe if (bufferRows>0){ myNames=rep("X",bufferRows) for(buf in 1:bufferRows){myNames[buf]<-paste(rep(" ",times=buf),collapse="")} bRows<-rep(c("z",0,0,"",0),times=bufferRows) bRows<-data.frame(matrix(bRows,nrow=(bufferRows),byrow=TRUE)) bRows[,1]<-myNames colnames(bRows)<-colnames(OMEGAS) plotOMEGAS<-data.frame(rbind(plotOMEGAS,bRows)) plotOMEGAS$OmegaTotal<-as.numeric(plotOMEGAS$OmegaTotal) plotOMEGAS$OmegaRatio<-as.numeric(plotOMEGAS$OmegaRatio) } #That's it for the data # now graphing #create basic ggplot, map food name against ratio - color according to Ratio, alpha according to total omega content/100g g.omega <- ggplot(plotOMEGAS,aes(x=EngName,y=OmegaRatio, fill=OmegaRatio, alpha=OmegaTotal)) + # flip coords so it reads vertically geom_bar(stat='identity') + coord_flip() + # add a color gradient that reflects the ratio scale_fill_continuous(guide=FALSE, low="orangered",high="green3", space="Lab",na.value="grey") + # scale the alpha 0.4-1 against omega % by weight scale_alpha_continuous(guide=FALSE, range = c(0.4, 1)) + # remove the legends and set a base theme theme_bw(base_family = "mono") + theme(legend.position="none") + # set the y scale scale_y_continuous(limits = c(-1.6-ratioLimit,ratioLimit+1), breaks=seq(-ratioLimit-1, ratioLimit+1, 2) ) # add text labels reflecting the omega content and position on the left g.omega <- g.omega + geom_text(aes(guide=FALSE,label = OmegaTotal, y=-1.6-ratioLimit, size=14, font_face="bold")) # write the title and axes - paste in the page numbers g.omega <- g.omega + xlab("Food Types\n[numbers indicate grams total Omega 3+6 per 100g Food]\n") + ylab(paste("\n 1:15 << Omega 3:6 Ratio >> 15:1 \n page",pg,"of",numPages,sep=" ")) + ggtitle("OMEGA 3:6 RATIO OF VARIOUS FOODS\n(TECHNICAL UNIVERSITY OF DENMARK : NFI)\n") + theme(plot.title = element_text(face="bold"), plot.margin=unit(c(1.5,1.5,1.5,1.5),"cm")) # you HAVE to use print - this writes the plot to the next page on the pdf print(g.omega) } # closes the pdf device dev.off()
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