\HeaderA{density-methods}{Density plot of a ExpressionSet object}{density.Rdash.methods}
\aliasA{density,ExpressionSet-method}{density-methods}{density,ExpressionSet.Rdash.method}
\aliasA{density.ExpressionSet}{density-methods}{density.ExpressionSet}
\keyword{methods}{density-methods}
\keyword{hplot}{density-methods}
\begin{Description}\relax
Creating density plot of sample intensities in a ExpressionSet object. It is equivalent to \LinkA{hist-methods}{hist.Rdash.methods}.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S4 method for signature 'ExpressionSet':
density(x, logMode=TRUE, xlab = NULL, ylab = "density", type = "l", 
        col=1:dim(x)[2], lty=1:dim(x)[2], lwd=1, xlim = NULL, index.highlight = NULL, color.highlight = 2, 
        symmetry = NULL, addLegend = TRUE, subset = 5000, seed = 123, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a \code{\LinkA{ExpressionSet}{ExpressionSet}} object
\item[\code{logMode}] determine whether the density plot is based on a log2 scale 
\item[\code{xlab}] xlab of the density plot 
\item[\code{ylab}] ylab of the density plot 
\item[\code{type}] parameter of plot function 
\item[\code{col}] line colors of the density plot 
\item[\code{lty}] line types of the density plot 
\item[\code{lwd}] line width of plot function 
\item[\code{xlim}] parameter of the plot function
\item[\code{index.highlight}] the column index of the highlighted density curve 
\item[\code{color.highlight}] color of highlighted density curve 
\item[\code{symmetry}] the boundary position suppose to be symmetric distributed  
\item[\code{addLegend}] whether add legend to the plot or not 
\item[\code{subset}] subset of rows used to plot. It can be an index vector, or the length of a random subset
\item[\code{seed}] the random seed for random subset
\item[\code{...}] additional parameters for \code{\LinkA{density}{density}} function 
\end{ldescription}
\end{Arguments}
\begin{SeeAlso}\relax
\code{\LinkA{LumiBatch-class}{LumiBatch.Rdash.class}}, \LinkA{hist-methods}{hist.Rdash.methods}, \code{\LinkA{density}{density}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load example data
data(example.lumi)

density(example.lumi)
\end{ExampleCode}
\end{Examples}

