\section{Scatter plots between phenotypes}\label{heatpairsFeatures}
\subsection{Preliminaries}

<<heatmap1>>=
library("HD2013SGI")

data("datamatrix",package="HD2013SGI")

dir.create(file.path("result","Figures"),showWarnings=FALSE,recursive=TRUE)
@

\subsection{Scatter plots of selected features}
The 6-dimensional array of log-transformed features is reshaped in a
2-dimensional matrix with columns for each selected feature.
<<distributionOfInteractions1,results=hide>>=
D = datamatrix$D
D = aperm(D, c(1,2,3,4,6,5))
dim(D) = c(prod(dim(D)[1:5]),dim(D)[6])
@

Scatter plots of the selected features are plotted using 1000 randomly selected double knock-down experiments.

<<distributionOfInteractions2,results=hide>>=
set.seed(712608)
S = sample(dim(D)[1],1000)
@
<<distributionOfInteractions3,echo=FALSE,results=hide>>=
pdf(file.path("result","Figures","heatpairsFeatures.pdf"),width=10,height=10)
@
<<distributionOfInteractions4,results=hide>>=
heatpairs(D[S,], cor.cex = 1.8,pch=20,main="")
@
<<distributionOfInteractions5,echo=FALSE,results=hide>>=
dev.off()

png(file.path("result","Figures","heatpairsFeatures.png"),width=800,height=800)
heatpairs(D[S,], cor.cex = 1.8,pch=20,main="")
dev.off()
@

\begin{center}
\includegraphics[width=0.7\textwidth]{result/Figures/heatpairsFeatures.png}
\end{center}