\HeaderA{ecdfplot}{Method implementing Lattice ECDF plots for flow data}{ecdfplot}
\aliasA{ecdfplot,formula,flowSet-method}{ecdfplot}{ecdfplot,formula,flowSet.Rdash.method}
\aliasA{panel.ecdfplot.flowset}{ecdfplot}{panel.ecdfplot.flowset}
\aliasA{prepanel.ecdfplot.flowset}{ecdfplot}{prepanel.ecdfplot.flowset}
\keyword{methods}{ecdfplot}
\keyword{dplot}{ecdfplot}
\begin{Description}\relax
This function creates Trellis displays of Empirical Cumulative
Distribution Functions from flow cytometry data using a formula
interface.
\end{Description}
\begin{Usage}
\begin{verbatim}

## methods for 'flowSet' objects

## S4 method for signature 'formula, flowSet':
ecdfplot(x, data, xlab, ylab,
         f.value = function(n) ppoints(ceiling(sqrt(n))),
         type = "l", as.table = TRUE,
         ...)

prepanel.ecdfplot.flowset(x, frames, channel, 
                          f.value, ...)
panel.ecdfplot.flowset(x, frames, channel,
                       f.value, ref = TRUE,
                       groups = NULL, subscripts,
                       col, col.points, pch, cex, 
                       alpha, col.line, lty, lwd, ...)

\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.  For the prepanel and panel
functions, a vector of names for the flow frames to be used in the
panel. 
\item[\code{data}] a \code{flowSet} object that serves as a source of data 
\item[\code{xlab, ylab}] Labels for data axes, with suitable defaults taken
from the formula 
\item[\code{f.value}] determines the number of points used in the plot
\code{\LinkA{ecdfplot}{ecdfplot}} for details.  
\item[\code{type}] type of rendering; by default lines are drawn 
\item[\code{as.table}] logical; whether to draw panels from top left 
\item[\code{ref}] logical; whether to add reference lines at 0 and 1 
\item[\code{frames}] environment containing frame-specific data 
\item[\code{channel}] expression involving names of columns in the data 
\item[\code{groups, subscripts}] grouping variable, if specified, and
subscripts indexing which frames are being used in the panel.  See
\code{\LinkA{xyplot}{xyplot}} for details.  
\item[\code{col, col.points, pch, cex, alpha, col.line, lty, lwd}] vector of
graphical parameters that are replicated for each group 
\item[\code{...}] more arguments, usually passed on to the underlying
lattice methods and the panel function. 
\end{ldescription}
\end{Arguments}
\begin{Section}{Methods}
\describe{

\item[ecdfplot] \code{signature(x = "formula", data = "flowSet")}:
plote empirical CDF for a given channel, with one or more samples
per panel

}
\end{Section}
\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)

ecdfplot(~ `FSC-H` | Patient, GvHD, f.value = ppoints(100))

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE)

ecdfplot(~ asinh(`FSC-H`) | Patient, GvHD, groups = Visit,
         strip = strip.custom(strip.names = TRUE),
         ref = FALSE, auto.key = list(columns = 4))

\end{ExampleCode}
\end{Examples}

