\HeaderA{hist-methods}{Density Estimate}{hist.Rdash.methods}
\aliasA{hist}{hist-methods}{hist}
\keyword{methods}{hist-methods}
\begin{Description}\relax
Plot the density estimates for each sample.

\emph{Usage}

\code{
hist(x, which = "", size = 0, transfo = log2, ylab = "density", xlab = "log intensity", type = "l", col = 1:6, ...)
}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{DataTreeSet}{DataTreeSet}} or \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.
\item[\code{which}] type of probes to be used, for details see \code{\LinkA{validData}{validData}}.
\item[\code{size}] length of sequence to be generated as subset.
\item[\code{transfo}] a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.
\item[\code{ylab}] a title for the y axis.
\item[\code{xlab}] a title for the x axis.
\item[\code{type}] type for the plot.
\item[\code{col}] colors to use for the different arrays.
\item[\code{...}] optional arguments to be passed to \code{plot}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Plots the non-parametric density estimates using values contained in the columns of 
slot \code{data}.

For a \code{\LinkA{DataTreeSet}{DataTreeSet}} object, data must first be attached using method 
\code{\LinkA{attachInten}{attachInten}}.
\end{Details}
\begin{Note}\relax
For exon array raw data only a limited number of samples can be displayed as density plot due to
memory limitations. To display all samples it is proposed to use function \code{\LinkA{root.density}{root.density}}
instead.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

## need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
hist(data.test3)
}

## optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)
\end{ExampleCode}
\end{Examples}

