R/plotPWF.R

In nadiadavidson/goseq: Gene Ontology analyser for RNA-seq and other length biased data

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#Description: Plot the probability weighting function 
#Notes: "auto" binsize tries to determine the best binsize to display the relationship b/w bias.data and %DE
#The "pwf" input can be either a list with the data.frame as an entry, or just the data.frame
#Author: Matthew Young
#Date Modified: 13/12/2010

plotPWF = function(pwf,binsize="auto",pwf_col=3,pwf_lwd=2,xlab="Biased Data in <binsize> gene bins.",ylab="Proportion DE",...){
		#We shouldn't try and plot NAs obviously...
		w=!is.na(pwf$bias.data)
		o=order(pwf$bias.data[w])
		#What is the total range in the fit?
		rang=max(pwf$pwf,na.rm=TRUE)-min(pwf$pwf,na.rm=TRUE)
		if(rang==0 & binsize=="auto") binsize=1000
		if(binsize=="auto"){
			#A low number of starting genes to bin, usually 100
			binsize=max(1,min(100,floor(sum(w)*.08)))
			resid=rang
			#Turn off warnings till we've worked out what we're doing
			oldwarn=options()$warn
			options(warn=-1)
			#Keep increasing the number of genes in each bin until the scatter around the lines reaches the cutoff.
			#Stop if we reach only 10 bins for the entire plot
			while(binsize<=floor(sum(w)*.1) & resid/rang>.001){
				binsize=binsize+100
				#Assign each gene a "bin number"
				splitter=ceiling(1:length(pwf$DEgenes[w][o])/binsize)
				#Determine the percentage DE in each bin
				de=sapply(split(pwf$DEgenes[w][o],splitter),mean)
				#Determine the average length in each bin
				binlen=sapply(split(as.numeric(pwf$bias.data[w][o]),splitter),mean)
				#Calculate the residuals, how much the binned data deviates from the PWF
				resid=sum((de-approx(pwf$bias.data[w][o],pwf$pwf[w][o],binlen)$y)^2)/length(binlen)
			}
			options(warn=oldwarn)
		}else{
			#Assign each gene a "bin number"
			splitter=ceiling(1:length(pwf$DEgenes[w][o])/binsize)
			#Determine the percentage DE in each bin
			de=sapply(split(pwf$DEgenes[w][o],splitter),mean)
			#Determine the average length in each bin
			binlen=sapply(split(as.numeric(pwf$bias.data[w][o]),splitter),mean)
		}
		#Now we've settled on a binsize, plot it
		#Did the user specify the labels? If so we can't put in the defaults or they'll be used twice and errors result.
		xlab=gsub("<binsize>",as.character(binsize),xlab)
		if("xlab"%in%names(list(...))){
			if("ylab"%in%names(list(...))){
				plot(binlen,de,...)
			}else{
				plot(binlen,de,ylab=ylab,...)
			}
		}else if("ylab"%in%names(list(...))){
			plot(binlen,de,xlab=xlab,...)
		}else{
			plot(binlen,de,xlab=xlab,ylab=ylab,...)
		}
		#Add the PWF
		lines(pwf$bias.data[w][o],pwf$pwf[w][o],col=pwf_col,lwd=pwf_lwd)
}