\section{Figures in paper}\label{Figures}
In this section all figures from the original publication are shown. In the next sections the R-code for the analysis is documented. A link to the respective section in which the figure is generated is given for each figure.
\subsection*{Figure 1cd}
The source code for this figure is in Section \ref{exampleSingleKDPhenotypes}.
\begin{center}
  \includegraphics[width=0.3\textwidth]{result/Figures/singleKnockDown-SETD8.pdf}
  \includegraphics[width=0.3\textwidth]{result/Figures/singleKnockDown-TCF20.pdf}
\end{center}

\subsection*{Figure 2a}
The source code for this figure is in Section \ref{QControlFeatures}.
\begin{center}
  \includegraphics[width=0.5\textwidth]{result/Figures/QCscatterFeaturesBetweenReplicates.pdf}
\end{center}

\subsection*{Figure 2bd}
The source code for this figure is in sections \ref{QControlFeatures} and \ref{QControlGenes}.
\begin{center}
  \includegraphics[width=0.45\textwidth]{result/Figures/QCreproducibilityOfFeatures.pdf}
  \includegraphics[width=0.45\textwidth]{result/Figures/QCreproducibilityOfTargetsiRNA.pdf}
\end{center}

\subsection*{Figure 2c}
The source code for this figure is in Section \ref{QControlGenes}.
\begin{center}
  \includegraphics[width=0.25\textwidth]{result/Figures/QCreproducibilityOfTargetsiRNAexample.pdf}
\end{center}

\subsection*{Figure 2e}
The source code for this figure is in Section \ref{smallCellNumber}.
\begin{center}
  \includegraphics[width=0.45\textwidth]{result/Figures/subsamplingNrInteractions.pdf}
\end{center}

\subsection*{Figure 3ab}
The source code for this figure is in Section \ref{exampleDoubleKDPhenotypes}.
\begin{center}
  \includegraphics[width=0.37\textwidth]{result/Figures/interaction-PHF16-SETD8.pdf}
  \includegraphics[width=0.37\textwidth]{result/Figures/interaction-SIN3A-RUVBL1.pdf}
\end{center}

\subsection*{Figure 3c}
The source code for this figure is in Section \ref{OverlapOfInteractions}.
\begin{center}
<<VennDiagram>>=
# load("result/Figures/Overlap.rda")
# print(Overlap)
@
\end{center}

\subsection*{Figure 4ac}
The source code for this figure is in Section \ref{heatmaps}.
\begin{center}
  \includegraphics[width=0.3\textwidth]{result/Figures/heatmapAll.pdf}
  \includegraphics[width=0.45\textwidth]{result/Figures/heatmapSelection.pdf}
\end{center}

\subsection*{Figure 4b}
The source code for this figure is in Section \ref{siRNAcorrelation}.
\begin{center}
\includegraphics[width=0.7\textwidth]{result/Figures/multidensityWithinDesignCorrelation.pdf}
\end{center}

% \clearpage
% 
% \begin{figure}
%   \centering
%   piplot categories
% %   \includegraphics[width=0.95\textwidth]{Figures/coComplexityHeatmap.pdf}
%   \mycaption{S1}
% \end{figure}
% 
% \clearpage
% 
% \begin{figure}
%   \centering
%   PCA on single knock down screen
% %   \includegraphics[width=0.5\textwidth]{Figures/MediatorOverlapYeastCorrelations.pdf}
%   \mycaption{S2}
% \end{figure}
% 

\subsection*{Figure S3}
The source code for this figure is in Section \ref{featureSelection}.
\begin{center}
  \includegraphics[width=0.45\textwidth]{result/Figures/FeatureSelectionInformationgain.pdf}
  \includegraphics[width=0.45\textwidth]{result/Figures/FeatureSelectionRatioPositive.pdf}
\end{center}

\subsection*{Figure S4}
The source code for this figure is in Section \ref{heatpairsFeatures}.
\begin{center}
  \includegraphics[width=0.6\textwidth]{result/Figures/heatpairsFeatures.png}
\end{center}

\subsection*{Figure S5}
The source code for this figure is in Section \ref{screenplot}.
\begin{center}
  \includegraphics[width=0.6\textwidth]{result/Figures/screenPlot.pdf}
\end{center}

\subsection*{Figure S6}
The source code for this figure is in Section \ref{distributionOfInteractions}.
\begin{center}
  \includegraphics[width=0.5\textwidth]{result/Figures/distributionOfInteractions.pdf}
\end{center}