\name{flowPlot}
\alias{flowPlot}
\alias{flowPlot,flowFrame-method}
\docType{methods}
\title{Standard Plots for Flow Cytometry Data
}

\description{
  A method that makes standard plots from a \code{flowFrame}. The user may also
  provide various \code{filter} or \code{filterResult} arguments to customize
  the plot.
}

\usage{

flowPlot(x, ...)

\S4method{flowPlot}{flowFrame}(x, child, filter = NULL,
         plotParameters = c("FSC-H","SSC-H"),
         logx = FALSE, logy = FALSE,
         parent, colParent="Grey", colChild="Blue",
         showFilter = TRUE, gate.fill = "transparent",
         gate.border = "black", xlab, ylab, xlim, ylim,
         \dots)
}

\arguments{
	\item{x}{An object of class \code{flowFrame} that contains the
	  data to be plotted.}
	\item{child}{An optional argument of class \code{filterResult}
	  that specifies a subset of the data that are included in the
	  \code{filterResult}} 
	\item{filter}{A \code{filter}, \code{filterResult} or
	  \code{filterResultList} object.}
	\item{plotParameters}{A vector of charactors defining the x and
	y variables in terms of columns in the data.}
	\item{logx, logy}{Logical controlling wheterh the corresponding
	variables will be log transfromed before passing to the panel
	function. Default to \code{FALSE}.} 
	\item{parent}{An optional argument of class \code{filterResult}
  	  that specifies a subset of the data that are inclueed in the
	  \code{filterResult}.}
	\item{colParent}{Specifying the color for \code{parent}. See
 	  \code{parent} above.}
	\item{colChild}{Specifies the color for \code{child}. See
	\code{chile} above.}
	\item{showFilter}{Logical, specifying whether to show the
  	  \code{filter}. }
	\item{gate.fill}{Specifies the fill color of the gate. Default
	  to \code{transparent}.}
	\item{gate.border}{Character or specifying the color of the gate
	  border. Default to \code{black}.}
	\item{xlab, ylab}{Labels for data axes.}
	\item{xlim, ylim}{Numeric vectors of length 2 specifying axis limits.}
	\item{\dots}{More arguments, usually passed on to the underlying
	  lattice methods.}
	
}
\details{
  The plot that is most commonly used in flow cytometry data analysis is usuall called
  a "dot plot". In common statistical language, we would call this a scatter plot. The
  basic idea is a 2-dimensional plot that shows the location of every cell in regard
  to the measurements made on it, for example, forward scatter vs side scatter. Most
  applications will, in addition to the data, want to show information about one or
  more filters (gates). Since there can be a very large number of cells in a sample,
  it is common to show a smoothed version of the data that doesn't involve registering
  every point on the graph.

}
\author{P. Haaland}

\keyword{methods}
\seealso{
\code{\link[flowCore:flowCore-package]{flowCore}}
}
\examples{

data(GvHD)
flowPlot(GvHD[["s5a01"]])
flowPlot(transform("SSC-H"=asinh,"FSC-H"=asinh) \%on\% GvHD[["s5a01"]])

}