\documentclass{article}

\title{Demo Sweave file}

\author{Martin}

\begin{document}
\SweaveOpts{concordance=TRUE}

\maketitle

<<>>=
data <- read.csv("comb_gnome_data.csv")
library(reshape2)
melted <- melt(data, id.vars=c("id", "group", "treatment"))
@


Let's get going! Load ggplot2:

<<fig=T>>=
library(ggplot2)
print(qplot(x=variable, y=value, color=treatment, geom="jitter", data=melted))
@



\end{document}