\HeaderA{plotQA.FCS}{Create a scatterplot summaryzing one (or two) parameter(s)
for several FCS objects stored in a  plate}{plotQA.FCS}
\keyword{hplot}{plotQA.FCS}
\begin{Description}\relax
Create a scatterplot summaryzing one (or two) parameter(s)
for several FCS objects stored in a  plate. The points are colored according to their position in the plate (row or column number.)
\end{Description}
\begin{Usage}
\begin{verbatim}
plotQA.FCS(data,varpos=c(1,2),FUN1=IQR,FUN2=NULL,col="row",nrow=8,ncol=12,ind=c(1:96),labeling=TRUE,...)                      
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] 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 data of the FCS object
\item[\code{FUN1}] function to summaryze the distribution of the data, e.g. mean, median, IQR, MODE
\item[\code{FUN2}] 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}] logical, draw plate position (default=TRUE)
\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.
 plotQA.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")

 ##Example II:
 ##Draw a a scatterplot of the mode and IQR values for the Foward scatter
 ##of each FCS file. 
 plotQA.FCS(flowcyt.data,varpos=c(1),FUN1=IQR,FUN2=MODE,nrow=8,ncol=10,ind=c(1:80),col="col",pch="*",labeling=TRUE,xlim=c(0,300),ylim=c(0,300),xlab="FSC mode",ylab="FSC IQR",main="FSC IQR vs.FSC mode by column")
 \end{ExampleCode}
\end{Examples}

