diff --git a/R/plotting_library.R b/R/plotting_library.R
new file mode 100644
index 000000000..e1ffc6d31
--- /dev/null
+++ b/R/plotting_library.R
@@ -0,0 +1,54 @@
+#!/broad/tools/apps/R-2.6.0/bin/Rscript
+
+args <- commandArgs(TRUE)
+fileToRead <- args[1]
+functionToRun <- args[2]
+functionSpecificArgs <- args[3]
+
+## load the function to run
+
+if ( funtionToRun == "PlotInterleavedRows" ) {
+### PLOT INTERLEAVED ROWS FUNCTION ###
+#  - expects a file of the form
+#
+# sample_a \t 0.8 \t 0.6 \t 0.5
+# sample_a \t 0 \t 1 \t 3
+# sample_b \t 0.5 \t 0.3 \t 0.1
+# sample_b \t 1 \t 2 \t 4
+# 
+# and an argument string
+#   x_label;y_label;plot_title;base_name_for_pdf
+#  - end of info -
+### PLOT INTERLEAVED ROWS FUNCTION ###
+PlotInterleavedRows <- function(inFile,args) {
+	arglist = unlist(strsplit(args,";"))
+	xlabel = arglist[1]
+	ylabel = arglist[2]
+	title = arglist[3]
+	outFileBase = arglist[4]
+	
+	allPoints <- as.matrix(read.table(inFile))
+	# set up colors
+	colors = rainbow(ncol(allPoints)-1,s=0.8,v=0.8,gamma=0.6,start=0.0,end=0.9)
+	styles = c(rep(1,ncol(allPoints)-1))
+	evalPoints = matrix(nrow=nrow(allPoints)/2,ncol=ncol(allPoints))
+	funcVal = matrix(nrow=nrow(allPoints)/2,ncol=ncol(allPoints))
+	# convert to two matrices by de-interleaving and transposing
+	for ( i in 1:(nrow(allPoints)/2) ) {
+		evalPoints[i,] <- allPoints[2*i,]
+		funcVal[i,] <- allPoints[2*i-1,]
+	}
+	
+	evalPoints <- t(evalPoints)
+	funcVal <- t(funcVal)
+	# plot and put legend on
+	pdf(paste(outFileBase,"_rplot",".pdf",sep=""))
+	matplot(evalPoints,funcVal,col=colors,lty=styles,"l",xlab=xlabel,ylab=ylabel)
+	legend("topright",funcVal[1,],lty=styles,col=colors)
+	# save
+	dev.off()
+}
+
+PlotInterleavedRows(fileToRead,functionSpecificArgs)
+
+}
\ No newline at end of file