\HeaderA{plotSpec-methods}{Plot mass spectra from the profile matrix}{plotSpec.Rdash.methods}
\aliasA{plotSpec}{plotSpec-methods}{plotSpec}
\aliasA{plotSpec,xcmsRaw-method}{plotSpec-methods}{plotSpec,xcmsRaw.Rdash.method}
\keyword{methods}{plotSpec-methods}
\keyword{hplot}{plotSpec-methods}
\keyword{iplot}{plotSpec-methods}
\begin{Description}\relax
Uses the pre-generated profile mode matrix to plot mass spectra
over a specified retention time range.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsRaw} object
\item[\code{ident}] logical, use mouse to identify and label peaks
\item[\code{vline}] numeric vector with locations of vertical lines
\item[\code{...}] arguments passed to \code{\LinkA{profRange}{profRange}}
\end{ldescription}
\end{Arguments}
\begin{Value}
If \code{ident == TRUE}, an integer vector with the indecies of
the points that were identified. Otherwise a two-column matrix
with the plotted points.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{plotSpec(object, ident = FALSE, vline = numeric(0), ...)}

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}}
\end{SeeAlso}

