\HeaderA{boxplot.FCS}{Create boxplots one parameter of one (or more) FCS object(s)}{boxplot.FCS}
\keyword{aplot}{boxplot.FCS}
\begin{Description}\relax
Produce box-and-whisker plot(s) of a single column variable specified from the
data of one (or more) FCS object(s).
\end{Description}
\begin{Usage}
\begin{verbatim}
boxplot.FCS(x, varpos=c(1),...)                      
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a list of  one (or more) FCS object(s) or a cytoSet object
\item[\code{varpos}] the numerical column variable position of the data of
the FCS object
\item[\code{...}] any other arguments are passed to the \code{\LinkA{boxplot}{boxplot}}
function
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If several FCS objects are supplied parallel boxplots will be
plotted.
Other options from the functions \code{\LinkA{plot}{plot}},
\code{\LinkA{boxplot}{boxplot}}.
\end{Details}
\begin{Value}
The \code{\LinkA{boxplot}{boxplot}} will output a list with the following components:
\begin{ldescription}
\item[\code{stats}] 
\item[\code{n}] 
\item[\code{conf}] 
\item[\code{out}] 
\item[\code{group}] 
\item[\code{names}] 
\end{ldescription}
  a vector of names for the groups
\end{Value}
\begin{Author}\relax
N. Le Meur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{boxplot}{boxplot}},
\code{\LinkA{boxplot.stats}{boxplot.stats}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
 ## Example I:
 require(rfcdmin)
 data(flowcyt.data)

 ## Draw a boxplot for the Foward SCatter parameter for the time points 1
 ## and 6 (in this experiment, each time point corresponds to a column of
 ## a 96 wells plates)
 mat <- matrix(c(1:2),1,2,byrow=TRUE)
 nf <- layout(mat,respect=TRUE)
 boxplot.FCS(flowcyt.data[1:8],varpos=c(1),col=c(1:8),main="FSC across stains time point 1",names=paste("stain",c(1:8),sep=""))
 boxplot.FCS(flowcyt.data[65:72],varpos=c(1),col=c(1:8),main="FSC across stains time point 9",names=paste("stain",c(1:8),sep=""))

 ##Example II:
 ## Read a serie of FCS files
 if (require(rfcdmin)) {

 ##obtaining the location of the fcs files in the data
  pathFiles<-system.file("bccrc", package="rfcdmin")
  drugFiles<-dir(pathFiles)

 ## reading in the FCS files
  drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
  }

 ##Draw a boxplot for the Foward SCatter parameter
 ##for the differents aliquots (of the same cell line)
 ##tested with different compounds. 
 boxplot.FCS(drugData,varpos=c(1),col=c(1:8),main="FSC of differents aliquots from the same cell line treated with different compounds.")

 \end{ExampleCode}
\end{Examples}

