\HeaderA{plotStringencyGene}{plot the Stringency related control probe profiles}{plotStringencyGene}
\keyword{methods}{plotStringencyGene}
\keyword{hplot}{plotStringencyGene}
\begin{Description}\relax
Plot the Stringency related control probe (Low-Stringency, Medium-Stringency and High-Stringency) profiles. Using getControlType function to view available stringency types.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotStringencyGene(controlData, lib = NULL, slideIndex = NULL, addLegend = TRUE, logMode = TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{controlData}] a LumiBatch object including control data or a control data data.frame 
\item[\code{lib}] the annotation library (for retrieving the gene name) 
\item[\code{slideIndex}] the slide index or ID corresponding to each sample 
\item[\code{addLegend}] whether add legend or not 
\item[\code{logMode}] whether show the data in log2 scale  
\item[\code{...}] other parameters used by default matplot function 
\end{ldescription}
\end{Arguments}
\begin{Value}
plot the picture and return TRUE if everything is OK
\end{Value}
\begin{Author}\relax
Pan Du
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{addControlData2lumi}{addControlData2lumi}}, \code{\LinkA{plotControlData}{plotControlData}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        controlFile <- system.file('doc', 'Control_Probe_Profile.txt', package='lumi')
        controlData <- getControlData(controlFile)
        plotStringencyGene(controlData)
\end{ExampleCode}
\end{Examples}

