\HeaderA{xyplot}{Method implementing Lattice ECDF plots for flow data}{xyplot}
\aliasA{panel.xyplot.flowset}{xyplot}{panel.xyplot.flowset}
\aliasA{prepanel.xyplot.flowset}{xyplot}{prepanel.xyplot.flowset}
\aliasA{splom}{xyplot}{splom}
\aliasA{splom,flowFrame,missing-method}{xyplot}{splom,flowFrame,missing.Rdash.method}
\aliasA{xyplot,flowFrame,missing-method}{xyplot}{xyplot,flowFrame,missing.Rdash.method}
\aliasA{xyplot,formula,flowFrame-method}{xyplot}{xyplot,formula,flowFrame.Rdash.method}
\aliasA{xyplot,formula,flowSet-method}{xyplot}{xyplot,formula,flowSet.Rdash.method}
\keyword{methods}{xyplot}
\keyword{dplot}{xyplot}
\begin{Description}\relax
These functions create Trellis scatter plots (a.k.a. dot plots in the
Flow Cytometry community) from flow cytometry data.
\end{Description}
\begin{Usage}
\begin{verbatim}

## methods for 'flowSet' objects

## S4 method for signature 'formula, flowSet':
xyplot(x, data,
       xlab, ylab,
       as.table = TRUE,
       prepanel = prepanel.xyplot.flowset,
       panel = panel.xyplot.flowset,
       pch = ".", smooth = TRUE,
       filter = NULL,
       filterResults = NULL,
       displayFilter = TRUE,
       ...)

## methods for 'flowFrame' objects

## S4 method for signature 'flowFrame, missing':
xyplot(x, data,
       xlab = time, ylab = "", time = "Time",
       layout,
       type = "l", smooth = FALSE,
       ...)

## S4 method for signature 'formula, flowFrame':
xyplot(x, data,
       smooth = TRUE, 
       panel = if (smooth) panel.smoothScatter else panel.xyplot,
       ...)

## S4 method for signature 'flowFrame, missing':
splom(x, data, 
      pscales = 0,
      smooth = TRUE, pch = ".",
      time = "Time", exclude.time = TRUE,
      panel = function(x, y, smooth, ...) {
          if (smooth) panel.smoothScatter(x, y, ...)
          else panel.xyplot(x, y, ...)
      },
      ...)


panel.xyplot.flowset(x, frames, channel.x, channel.y,
             channel.x.name, channel.y.name, 
             filter = NULL, filterResults = NULL, displayFilter = TRUE,
             pch, smooth, ...)

prepanel.xyplot.flowset(x, frames, channel.x, channel.y, ...)

\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.  In
\code{prepanel.xyplot.flowset} and \code{panel.xyplot.flowset},
names of flow frames. 
\item[\code{data}] a \code{flowSet} or \code{flowFrame} object that serves
as the source of data 
\item[\code{smooth}] logical.  If \code{TRUE},
\code{\LinkA{panel.smoothScatter}{panel.smoothScatter}}
is used to display a partially smoothed version of the data.
Otherwise, points are plotted as in a standard scatter plot.

\item[\code{xlab, ylab}] Labels for data axes, with suitable defaults taken
from the formula 
\item[\code{pch}] the plotting character used when \code{smooth=FALSE}
\item[\code{type}] type of rendering; see
\code{\LinkA{panel.xyplot}{panel.xyplot}} for details. 
\item[\code{prepanel}] the prepanel function.  See
\code{\LinkA{xyplot}{xyplot}} 
\item[\code{panel}] the panel function.  See
\code{\LinkA{xyplot}{xyplot}} 
\item[\code{filter}] A \LinkA{filter}{filter} object.  Ignored
when \code{filterResults} is not \code{NULL}. 
\item[\code{filterResults}] A
\LinkA{filterResult}{filterResult} object, that
is the result of applying a filter on each frame in \code{data}.  If
this is \code{NULL} but \code{filter} is not, it will be created on
the fly by applying \code{filter} to each frame.  
\item[\code{displayFilter}] logical or list.  If \code{TRUE}, an attempt is
made to display the geometric boundaries of \code{filter} (if
specified) in the plot.  The same holds if \code{displayFilter} is a
list, but in that case the components are interpreted as graphical
parameters to be passed on to
\code{\LinkA{panel.polygon}{panel.polygon}}

\item[\code{time}] A character string giving the name of the column
recording time. 
\item[\code{exclude.time}] logical, specifying whether to exclude the time
variable from a scatter plot matrix. 
\item[\code{as.table, pscales, layout}] These arguments are passed unchanged
to the corresponding methods in lattice, and are listed here only
because they provide different defaults.  See documentation for the
original methods for details.

\item[\code{channel.x, channel.y}] expressions defining the x and y
variables in terms of columns in the data.  Can involve functions
or multiple columns from the data. 
\item[\code{channel.x.name, channel.y.name}] character strings giving
corresponding names, used to match filter parameters if applicable.

\item[\code{frames}] an environment containing frame-specific data
\item[\code{...}] more arguments, usually passed on to the underlying
lattice methods. 
\end{ldescription}
\end{Arguments}
\begin{Section}{Methods}
\describe{

\item[xyplot] \code{signature(x = "formula", data = "flowSet")}:
creates scatter plots (a.k.a. dot plots) of a pair of channels


\item[xyplot] \code{signature(x = "flowFrame", data = "missing")}:
produces diagnostic time series plots of all channels against
time.


\item[xyplot] \code{signature(x = "formula", data = "flowFrame")}:
more general scatter plots from a \code{flowFrame} object.  The
formula can be fairly general.


\item[splom] \code{signature(x = "flowFrame", data = "missing")}:
draws a scatter plot matrix of all channels (excluding time, by
default) of a \code{flowFrame} object.


}
\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)

## simple bivariate scatter plot (a.k.a. dot plot)
## by default ('smooth=TRUE') panel.smoothScatter is used

xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = GvHD, 
       layout = c(7, 5))

xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit,
       data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
       layout = c(7, 5))

## version without smooth

xyplot(`SSC-H` ~ `FSC-H` | Visit + Patient, data = GvHD, 
       smooth = FALSE, strip = strip.custom(strip.names = TRUE))

## several examples with time on the X axis

xyplot(`FSC-H` ~ Time | Visit, GvHD, 
       smooth = FALSE, type = "l", 
       subset = (Patient == 5))

xyplot(`FSC-H` ~ Time | Patient:Visit, GvHD, 
       smooth = FALSE, type = "l",
       strip = FALSE, strip.left = TRUE,
       aspect = "xy")

## combine plots for two channels

ssc.time <- 

    xyplot(`SSC-H` ~ Time | factor(Patient):factor(Visit), GvHD, 
           smooth = FALSE, type = "l",
           strip = FALSE,
           strip.left = strip.custom(horizontal = TRUE),
           par.strip.text = list(lines = 3),
           between = list(y = rep(c(0, 0.5), c(6, 1))),
           scales = list(x = list(axs = "i"), y = list(draw = FALSE)),
           layout = c(1, 35))

fsc.time <- 

    xyplot(`FSC-H` ~ Time | factor(Patient):factor(Visit), GvHD, 
           smooth = FALSE, type = "l",
           strip = FALSE,
           strip.left = strip.custom(horizontal = TRUE),
           par.strip.text = list(lines = 3),
           between = list(y = rep(c(0, 0.5), c(6, 1))),
           scales = list(x = list(axs = "i"), y = list(draw = FALSE)),
           layout = c(1, 35))

plot(fsc.time, split = c(1, 1, 2, 1))
plot(ssc.time, split = c(2, 1, 2, 1), newpage = FALSE)

## saving plots as variables allows more manipulation

plot(update(fsc.time[29:35], layout = c(1, 7)),
     split = c(1, 1, 1, 2))

plot(update(ssc.time[29:35], layout = c(1, 7)),
     split = c(1, 2, 1, 2), newpage = FALSE)

## scatter plot matrix of individual flowFrames

splom(GvHD[["s10a07"]], smooth = FALSE)

splom(GvHD[["s10a07"]], smooth = FALSE,
      prepanel.limits = function(x) quantile(as.numeric(x), c(0.0, 0.99)))

## time plot of individual flowFrames

xyplot(GvHD[["s5a07"]], time = "Time")

xyplot(`FSC-H` + `SSC-H` + `FL1-H` ~ Time, GvHD[["s5a07"]],
       aspect = "xy", outer = TRUE,
       scales = list(y = "free"),
       type = "l", smooth = FALSE)

xyplot(`FSC-H` ~ `SSC-H`, GvHD[["s5a01"]], nbin = 100)

## displaying filters

n2gate <- norm2Filter("SSC-H", "FSC-H")

xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = GvHD,
       filter = n2gate, ## displayFilter = TRUE,
       layout = c(7, 5))

xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit,
       data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
       smooth = FALSE,
       filter = n2gate, ## displayFilter = list(border = "black"),
       layout = c(7, 5))

xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit,
       data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
       subset = Patient == "6",
       filter = rectangleGate("FSC-H"=c(5.5, 7),"SSC-H"=c(4, 6.5)),
       displayFilter = list(lwd = 3))

n2gate.results <- filter(GvHD, n2gate %on% transform("SSC-H"=asinh,"FSC-H"=asinh))

xyplot(`SSC-H` ~ `FSC-H` | Visit, data = GvHD,
       subset = Patient == "6",
       filterResults = n2gate.results, smooth = FALSE)

xyplot(`SSC-H` ~ `FSC-H` | Visit,
       data = GvHD,
       subset = Patient == "6",
       smooth = FALSE,
       filter = n2gate,
       filterResults = n2gate.results,
       displayFilter = list(lwd = 0.5))

xyplot(`SSC-H` ~ `FSC-H` | Visit,
       data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
       subset = Patient == "6",
       smooth = FALSE,
       filter = rectangleGate("FSC-H"=c(5.5, 7),"SSC-H"=c(4, 6.5)),
       filterResults = n2gate.results,
       displayFilter = list(border = 'red'))

\end{ExampleCode}
\end{Examples}

