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+#!/usr/bin/env Rscript
+
+# Usage:
+#
+# octane.R control.csv variable.csv
+#
+# Output will be placed in Rplots.pdf
+#
+# Remember: on Octane, higher is better!
+
+library(ggplot2)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+# Reading in data.
+control <- read.table(args[1], sep=",", header=TRUE)
+variable <- read.table(args[2], sep=",", header=TRUE)
+
+# Pulling out columns that we want to plot.
+# Not totally necessary.
+ctrl <- control$Score..version.9.
+var <- variable$Score..version.9.
+
+# Concatenating the values we want to plot.
+score <- c(ctrl, var)
+# Creating a vector of labels for the data points.
+label <- c(rep("control", length(ctrl)), rep("variable", length(var)))
+
+# Creating a data frame of the score and label.
+data <- data.frame(label, score)
+
+# Now plotting!
+ggplot(data, aes(label, score, color=label, pch=label)) +
+ # Adding boxplot without the outliers.
+ geom_boxplot(outlier.shape=NA) +
+ # Adding jitter plot on top of the boxplot. If you want to spread the points
+ # more, increase jitter.
+ geom_jitter(position=position_jitter(width=0.05))