[mcq.plot.peptide.reproducibility] => ggplot ok

MassChroqR/R/mcq_plot_peptide_reproducibility.R

@@ -23,32 +23,24 @@ mcq.plot.peptide.reproducibility<- function (object, file=NULL) {
 			nb.prot.kept <- length(unique(object@proteins$protein[object@proteins$peptide %in% names.pep.kept]))
 			nb.prot.lost <- c(nb.prot.lost, nb.prot.tot-nb.prot.kept)		
 		}
+		
+		nb.prot.lost.norm <- floor(nb.prot.lost * max(nb.pepz.lost)/max(nb.prot.lost))
 
 		df1 <- data.frame(x=seq(0,100, by=5),y=nb.pepz.lost,z=rep("peptides-mz",length(nb.pepz.lost)))
-		df2 <- data.frame(x=seq(0,100, by=5),y=nb.prot.lost,z=rep("proteins",length(nb.prot.lost)))
+		df2 <- data.frame(x=seq(0,100, by=5),y=nb.prot.lost.norm,z=rep("proteins",length(nb.prot.lost.norm)))
 		df3 <- rbind(df1,df2)
-
+		
+		
+	
 		if (is.null(file)){
 			par(ask=FALSE)
 		}
 		else{
 			pdf(file, title=gsub('.pdf$','',file), width=15)
 		}
-		#par(mfrow=c(1,2))
-		#hist(count, main=c("Distribution of the number of injections in which", "a peptide-mz was quantified"), xlab="Number of injections", nclass=nbsample, border="darkblue", ylab="Number of peptides-mz")
-		#par(mar=c(6,4,2,5))
-		#plot(nb.pepz.lost~seq(0,100, by=5), type="b", ylab="Number of peptides-mz lost", xlab=c("% of NA tolerated per peptide-mz"), col="red")
-		#par(new=TRUE)
-		#plot(nb.prot.lost~seq(0,100, by=5), axes=FALSE, xlab="", ylab="", col="blue", type="b")
-		#axis(4, labels=TRUE)
-		#mtext("Number of proteins lost",side=4, line=2.5)
-		#legend("topright", pch=1, col=c("red", "blue"), legend=c("Peptides-mz", "Proteins"), bty="n")
-
-		#par(mar=c(5,4,4,2))
-		#par(new=FALSE)
-		#par(mfrow=c(1,1))
+
+		# plots representation
 		
-		# ggplot2
 		plot1 <- ggplot(df, aes(x=value)) +
 		geom_histogram(binwidth=0.5) +
 		theme(panel.background=element_blank(),plot.title = element_text(hjust=0.5)) +
@@ -58,7 +50,11 @@ mcq.plot.peptide.reproducibility<- function (object, file=NULL) {
 
 		plot2 <- ggplot(df3, aes(x=x,y=y,colour=z)) +
 		geom_point() +
-		geom_line()
+		geom_line() +
+		scale_x_continuous("% of NA tolerated per peptide-mz") +
+		scale_y_continuous("Number of peptides-mz lost", sec.axis=sec_axis(~./(max(nb.pepz.lost)/max(nb.prot.lost)),name="Number of proteins lost")) +
+		theme(legend.position = "none", axis.title.y = element_text(color = "red"),axis.text.y = element_text(color = "red"), axis.text.y.right = element_text(color = "cyan3"),axis.title.y.right = element_text(color = "cyan3"))
+		
 		grid.arrange(plot1, plot2, ncol=2, nrow = 1)
 		
 		if (!is.null(file)){