\HeaderA{plotChrom-methods}{Plot extracted ion chromatograms from the profile matrix}{plotChrom.Rdash.methods}
\aliasA{plotChrom}{plotChrom-methods}{plotChrom}
\aliasA{plotChrom,xcmsRaw-method}{plotChrom-methods}{plotChrom,xcmsRaw.Rdash.method}
\keyword{methods}{plotChrom-methods}
\keyword{hplot}{plotChrom-methods}
\keyword{iplot}{plotChrom-methods}
\begin{Description}\relax
Uses the pre-generated profile mode matrix to plot averaged or
base peak extracted ion chromatograms over a specified mass range.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsRaw} object
\item[\code{base}] logical, plot a base-peak chromatogram
\item[\code{ident}] logical, use mouse to identify and label peaks
\item[\code{fitgauss}] logical, fit a gaussian to the largest peak
\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. If \code{fitgauss == TRUE}, a
\code{nls} model with the fitted gaussian. Otherwise a two-column
matrix with the plotted points.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{plotChrom(object, base = FALSE, ident = FALSE,
                  fitgauss = FALSE, vline = numeric(0), ...)}

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

