Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. Journal of computational biology. 2003;10(6):857-68 using only the Base graphics system in R.
Data can be downloaded from here (if it doesn't work, use Google's cache).
I imported the file in a spreadsheet and then I copied & pasted it in R.
jcb.scores = read.delim("clipboard")
attach(jcb.scores)
pdf("recomb_scores.pdf")
par(las =1) # To have horizontal labels for axes 2 and 4
plot(y~sort(SVM.pairwise.ROC, decreasing = TRUE), pch = 3, cex = 0.5,
xlab = "AUC", ylab = "Number of families", axes = FALSE,
xlim = c(0,1), ylim = c(0,60))
lines(y~sort(SVM.pairwise.ROC, decreasing = TRUE), lty = 1)
points(y~sort(FPS.ROC, decreasing = TRUE), pch = 4, cex = 0.5)
lines(y~sort(FPS.ROC, decreasing = TRUE), lty = 2)
points(y~sort(SVM.Fisher.ROC, decreasing = TRUE), pch = 8, cex = 0.5)
lines(y~sort(SVM.Fisher.ROC, decreasing = TRUE), lty = 3)
points(y~sort(SAM.ROC, decreasing = TRUE), pch = 0, cex = 0.5)
lines(y~sort(SAM.ROC, decreasing = TRUE), lty = 4)
points(y~sort(PSI.BLAST.ROC, decreasing = TRUE), pch = 15, cex = 0.5)
lines(y~sort(PSI.BLAST.ROC, decreasing = TRUE), lty = 5)
axis(1, at = seq(0,1,0.2), labels = c(0,0.2,0.4,0.6,0.8,1), tcl = 0.25, pos = 0) # tcl = 0.25 small ticks toward the curve
axis(2, at = c(0,10,20,30,40,50,60), labels=c(0,10,20,30,40,50,60), tcl= 0.25 , pos = 0)
axis(2, at = c(0,10,20,30,40,60), tcl= 0.25,labels = F, pos = 0)
axis(3, tick = T, tcl= 0.25, labels = F, pos = 60)
axis(4, at = c(0,10,20,30,40,50), tcl= 0.25, labels = F, pos = 1)
axis(4, at = c(0,10,20,30,40,60), tcl= 0.25, labels = F, pos = 1)
# To locate the legend interactively
xy.legend = locator(1)
# right-justifying a set of labels: thanks to Uwe Ligges
temp <- legend(xy.legend, legend = c("SVM-pairwise", "FPS","SVM-Fisher", "SAM","PSI-BLAST"), text.width = strwidth("SVM-pairwise"), xjust = 1, yjust = 1, lty = c(1,2,3,4,5), pch = c(3,4,8,0,15), bty = "n", cex = 0.8, title = "")
dev.off()
detach(jcb.scores)The original image:
My version of the image (not exacly identical but...):
