\HeaderA{plot.xcmsEIC}{Plot extracted ion chromatograms from multiple files}{plot.xcmsEIC}
\aliasA{plot, plot-methods}{plot.xcmsEIC}{plot, plot.Rdash.methods}
\keyword{methods}{plot.xcmsEIC}
\keyword{hplot}{plot.xcmsEIC}
\begin{Description}\relax
Batch plot a list of extracted ion chromatograms to the current
graphics device.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] the \code{xcmsEIC} object
\item[\code{y}] optional \code{xcmsSet} object with peak integration data
\item[\code{groupidx}] either character vector with names or integer vector with
indicies of peak groups for which to plot EICs

\item[\code{sampleidx}] either character vector with names or integer vector with
indicies of samples for which to plot EICs

\item[\code{rtrange}] a two column matrix with minimum and maximum retention times
between which to return EIC data points

if it has the same number of rows as the number groups in the
\code{xcmsEIC} object, then \code{sampleidx} is used to subset
it. otherwise, it is repeated over the length of \code{sampleidx}

it may also be a single number specifying the time window around
the peak for which to plot EIC data

\item[\code{col}] color to use for plotting extracted ion chromatograms. if missing
and \code{y} is specified, colors are taken from
\code{unclass(sampclass(y))} and the default palette

if it is the same length as the number groups in the \code{xcmsEIC}
object, then \code{sampleidx} is used to subset it. otherwise,
it is repeated over the length of \code{sampleidx}

\item[\code{legtext}] text to use for legend. if \code{NULL} and \code{y} is specified,
legend text is taken from the sample class information found
in the \code{xcmsSet}

\item[\code{peakint}] logical, plot integrated peak area with darkened lines (requires
that \code{y} also be specified)

\item[\code{sleep}] seconds to pause between plotting EICs
\item[\code{...}] other graphical parameters
\end{ldescription}
\end{Arguments}
\begin{Value}
A \code{xcmsSet} object.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[x = "xcmsEIC"] \code{
plot.xcmsEIC(x, y, groupidx = groupnames(x), sampleidx = sampnames(x), rtrange = x@rtrange, 
             col = rep(1, length(sampleidx)), legtext = NULL, peakint = TRUE, sleep = 0, ...)}


}
\end{Section}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsEIC-class}{xcmsEIC.Rdash.class}},
\code{\LinkA{png}{png}},
\code{\LinkA{pdf}{pdf}},
\code{\LinkA{postscript}{postscript}},
\end{SeeAlso}

