\HeaderA{plotPeaks-methods}{Plot a grid of a large number of peaks}{plotPeaks.Rdash.methods}
\aliasA{plotPeaks}{plotPeaks-methods}{plotPeaks}
\aliasA{plotPeaks,xcmsRaw-method}{plotPeaks-methods}{plotPeaks,xcmsRaw.Rdash.method}
\keyword{methods}{plotPeaks-methods}
\keyword{hplot}{plotPeaks-methods}
\begin{Description}\relax
Plot extracted ion chromatograms for many peaks simultaneously, 
indicating peak integration start and end points with vertical
grey lines.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsRaw} object
\item[\code{peaks}] matrix with peak information as produced by \code{\LinkA{findPeaks}{findPeaks}}

\item[\code{figs}] two-element vector describing the number of rows and the number
of columns of peaks to plot, if missing then an approximately
square grid that will fit the number of peaks supplied

\item[\code{width}] width of chromatogram retention time to plot for each peak

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is intended to help graphically analyze the results
of peak picking. It can help estimate the number of false positives
and improper integration start and end points. Its output is very
compact and tries to waste as little space as possible. Each plot
is labeled with rounded m/z and retention time separated by a
space.
\end{Details}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{plotPeaks(object, peaks, figs, width = 200)}

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}},
\code{\LinkA{findPeaks}{findPeaks}},
\code{\LinkA{split.screen}{split.screen}}
\end{SeeAlso}

