\HeaderA{plot2sets.FCS}{Create a scatterplot to summaryze and compare two series of FCS
objects}{plot2sets.FCS}
\keyword{hplot}{plot2sets.FCS}
\begin{Description}\relax
Create a scatterplot to summaryze and compare 1 paraneter from two
series of FCS objects stored in 2 different plates. The points are colored according to their position in the plate (row or column number.)
\end{Description}
\begin{Usage}
\begin{verbatim}
plot2sets.FCS(data1,data2,varpos=c(1),FUN,nrow=8,ncol=12,ind=c(1:96),col="row",labeling=TRUE,...)                      
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data1}] a list of fluorescent data from one (or more) FCS
object(s) or a cytoset
\item[\code{data2}] a list of fluorescent data from one (or more) FCS
object(s) or a cytoset
\item[\code{varpos}] the numerical column variable position of the FCS objects
\item[\code{FUN}] function to summaryze the distribution of the data, e.g. mean, median, IQR, MODE
\item[\code{col}] 
\item[\code{nrow}] numeric, number of rows per plate
\item[\code{ncol}] numeric, number of columns per plate
\item[\code{ind}] numeric vector, index of the wells to be plotted
\item[\code{labeling}] 
\item[\code{...}] any other arguments are passed to the \code{\LinkA{plot}{plot}}
function
\end{ldescription}
\end{Arguments}
\begin{Value}
None.
\end{Value}
\begin{Author}\relax
Nolwenn Le Meur
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{plot}{plot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  ##Example I:
  ##data(flowcyt.data)

 ##Draw a scatterplot of the median values
 ##of the Foward scatter and the Side scatter parameters
 ##of each FCS file. The files correspond to samples store in a 96 well plate.
 ##plot2sets.FCS(flowcyt.data,varpos=c(1,2),FUN1=median,nrow=8,ncol=10,ind=c(1:80),col="row",pch="*",labeling=FALSE,xlim=c(0,300),ylim=c(0,300),main="FSCmedian vs.SSCmedian by row",xlab="SSC median",ylab="FSC median")

 
 \end{ExampleCode}
\end{Examples}

