\HeaderA{splom}{Method implementing Lattice scatter plot matrices for flow data.}{splom}
\aliasA{panel.splom.flowframe}{splom}{panel.splom.flowframe}
\aliasA{splom,flowFrame,missing-method}{splom}{splom,flowFrame,missing.Rdash.method}
\keyword{methods}{splom}
\keyword{dplot}{splom}
\begin{Description}\relax
This function create Trellis scatter plots matrices (splom) from flow
cytometry data.
\end{Description}
\begin{Usage}
\begin{verbatim}

## S4 method for signature 'flowFrame, missing':
splom(
    x,
    data, 
    pscales,
    time,
    exclude.time=TRUE,
    names=FALSE,
    ...)

panel.splom.flowframe(
    x,
    frame,
    ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A formula describing the structure of the plot and the
variables to be used in the display. 
\item[\code{data, frame}] A \code{\LinkA{flowFrame}{flowFrame}}
object that serves as the source of data. 
\item[\code{pscales}] This arguments is passed unchanged to the
corresponding methods in lattice, and is listed here only because it
provides a different default.  See documentation for the original
methods for details. 
\item[\code{time}] A character string giving the name of the data column
recording time. If not provided, we try to guess from the available
parameters. 
\item[\code{exclude.time}] Logical, specifying whether to exclude the time
variable from a scatter plot matrix. Defaults to \code{TRUE}. 
\item[\code{names}] Logical specifying wether gate names should be added to
the plot. Currently, this feature is not supported for splom plots. 
\item[\code{...}] More arguments, usually passed on to the underlying
lattice methods. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The function draws a scatter plot matrix of the data for each flow
parameter in a \code{flowFrame}. For the most, one can think about
this as a rectangular arrangement of separate
\code{\LinkA{xyplots}{xyplots}}, and most of that functionality is also
available here. To be more precise, the function repeatedly calls
\code{panel.xyplot.flowframe} to do the actual plotting. Please see
its documentation for details.
\end{Details}
\begin{Section}{Methods}
\describe{

\item[splom] \code{signature(x = "flowFrame", data = "missing")}:
Creates a scatter plot matrix for a whole \code{flowFrame}. The
actual plotting is done by \code{\LinkA{panel.xyplot.flowframe}{panel.xyplot.flowframe}},
so most additional arguments from the regular \code{xyplot} are
also valid here. 

}
\end{Section}
\begin{Author}\relax
F. Hahne, D. Sarkar
\end{Author}
\begin{SeeAlso}\relax
Not all standard lattice arguments will have the intended
effect, but many should.  For a fuller description of possible
arguments and their effects, consult documentation on lattice.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(GvHD)

tf <- transformList(colnames(GvHD)[3:7], asinh)
dat <- tf %on% GvHD[[3]]

## scatter plot matrix of individual flowFrames
lattice.options(panel.error=NULL)
splom(dat)

splom(dat[,1:3], smooth = FALSE)

## displaying filters
rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(300,700),
"FL1-H"=c(2,4), "FL2-A"=c(4,7))
splom(dat, filter=rg)

splom(dat, filter=rectangleGate("FSC-H"=c(400,800)))

splom(dat[,1:4], smooth = FALSE, filter=norm2Filter("FSC-H", "SSC-H", scale=1.5))

\end{ExampleCode}
\end{Examples}

