\HeaderA{plot-methods}{Plot of a LumiBatch object}{plot.Rdash.methods}
\aliasA{plot,LumiBatch,missing-method}{plot-methods}{plot,LumiBatch,missing.Rdash.method}
\aliasA{plot,LumiBatch-method}{plot-methods}{plot,LumiBatch.Rdash.method}
\aliasA{plot.LumiBatch}{plot-methods}{plot.LumiBatch}
\keyword{methods}{plot-methods}
\keyword{hplot}{plot-methods}
\begin{Description}\relax
Creating quality control plots of a LumiBatch object
\end{Description}
\begin{Usage}
\begin{verbatim}
## S4 method for signature 'LumiBatch, missing':
plot(x, what = c("density", "boxplot", "pair", "MAplot", "sampleRelation", "outlier", "cv"), main, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a LumiBatch object returned by \code{\LinkA{lumiQ}{lumiQ}} 
\item[\code{what}] one of the six kinds of QC plots 
\item[\code{main}] the title of the QC plot 
\item[\code{...}] additional parameters for the corresponding QC plots 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The parameter "what" of \code{plot} function controls the type of QC plots,
which includes:
\describe{
\item[\bold{density}:] the density plot of the chips, see \code{\LinkA{hist-methods}{hist.Rdash.methods}}
\item[\bold{boxplot}:] box plot of the chip intensities, see \code{\LinkA{boxplot-methods}{boxplot.Rdash.methods}}
\item[\bold{pair}:] the correlation among chips, plot as a hierarchical tree, see \code{\LinkA{pairs-methods}{pairs.Rdash.methods}}
\item[\bold{MAplot}:] the MAplot between chips, see \code{\LinkA{MAplot-methods}{MAplot.Rdash.methods}}
\item[\bold{sampleRelation}:] plot the sample relations. See \code{\LinkA{plotSampleRelation}{plotSampleRelation}}
\item[\bold{outlier}:] detect the outliers based on the sample distance to the center. See 
\code{\LinkA{detectOutlier}{detectOutlier}}
\item[\bold{cv}:] the density plot of the coefficients of variance of the chips. See \code{\LinkA{estimateLumiCV}{estimateLumiCV}}
}
\end{Details}
\begin{SeeAlso}\relax
\code{\LinkA{LumiBatch-class}{LumiBatch.Rdash.class}}, \code{\LinkA{hist-methods}{hist.Rdash.methods}}, \code{\LinkA{boxplot-methods}{boxplot.Rdash.methods}}, \code{\LinkA{MAplot-methods}{MAplot.Rdash.methods}},
\code{\LinkA{pairs-methods}{pairs.Rdash.methods}}, \code{\LinkA{plotSampleRelation}{plotSampleRelation}}, \code{\LinkA{estimateLumiCV}{estimateLumiCV}}, \code{\LinkA{detectOutlier}{detectOutlier}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

## load example data
data(example.lumi)

## Quality control estimation
lumi.Q <- lumiQ(example.lumi)

## summary
summary(lumi.Q)

## plot the density
plot(lumi.Q, what='density')

## plot the pairwise sample correlation
plot(lumi.Q, what='pair')

## plot the pairwise MAplot
plot(lumi.Q, what='MAplot')

## sample relations
plot(lumi.Q, what='sampleRelation', method='mds', color=c('100US', '95US:5P', '100US', '95US:5P'))

## detect outlier based on the distance to the mean profile
plot(lumi.Q, what='outlier')

## Density plot of coefficient of variance
plot(lumi.Q, what='cv')

\end{ExampleCode}
\end{Examples}

