\name{boxplot.FCS}
\alias{boxplot.FCS}

\title{Create boxplots one parameter of one (or more) FCS object(s)}
\description{
  Produce box-and-whisker plot(s) of a single column variable specified from the
  data of one (or more) FCS object(s).
}
\usage{
boxplot.FCS(x, varpos=c(1),groups=NULL, xlab, ylab, col,
alternating=TRUE, do.out = FALSE, ...)                      
}

\arguments{
  \item{x}{a list of  one (or more) FCS object(s) or a cytoSet object}

  \item{varpos}{the numerical column variable position of the data of
    the FCS object}
  
 \item{groups}{a variable or expression to be evaluated in the data
    frame specified by 'data', expected to act as a grouping variable
    within each panel, typically used to distinguish different groups by
    varying graphical parameters like color and line type}

  
  \item{xlab}{a title for the x axis}
  
  \item{ylab}{a title for the y axis}

  \item{col}{The colors for lines and points. Multiple colors can be
    specified so that each point can be given its own color. If there
    are fewer colors than points they are recycled in the standard
    fashion. Lines will all be plotted in the first colour specified.}

  \item{alternating}{logical specifying whether axis labels should
    alternate from one side
    of the group of panels to the other (for more details see \code{\link[lattice]{xyplot}})}
	     
  \item{do.out}{logical to specify if the outlier values should be
    displayed (default is FALSE)}
  
  \item{...}{any other arguments are passed to the \code{\link{boxplot}}
  function}
}  

\details{
  If several FCS objects are supplied parallel boxplots will be
  plotted.
  Other options from the functions \code{\link{plot}},
  \code{\link{boxplot}}.
}

\value{
  The \code{\link{boxplot}} will output a list with the following components:
  \item{stats} 	a matrix, each column contains the extreme of the lower whisker, the lower hinge, the median, the upper hinge and the extreme of the upper whisker for one group/plot.
  \item{n} 	a vector with the number of observations in each group.
  \item{conf} 	a matrix where each column contains the lower and upper extremes of the notch.
  \item{out} 	the values of any data points which lie beyond the extremes of the whiskers.
  \item{group} 	a vector of the same length as out whose elements indicate which group the outlier belongs to
  \item{names} 	a vector of names for the groups
}

\author{N. Le Meur}


\seealso{\code{\link{boxplot}},
  \code{\link{boxplot.stats}}}


\examples{

 ## 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.")

 }

\keyword{aplot}