\HeaderA{plotSurf-methods}{Plot profile matrix 3D surface using OpenGL}{plotSurf.Rdash.methods}
\aliasA{plotSurf}{plotSurf-methods}{plotSurf}
\aliasA{plotSurf,xcmsRaw-method}{plotSurf-methods}{plotSurf,xcmsRaw.Rdash.method}
\keyword{methods}{plotSurf-methods}
\keyword{hplot}{plotSurf-methods}
\keyword{iplot}{plotSurf-methods}
\begin{Description}\relax
This method uses the rgl package to create interactive three
dimensonal representations of the profile matrix. It uses the terrain
color scheme.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsRaw} object
\item[\code{log}] logical, log transform intensity
\item[\code{aspect}] numeric vector with aspect ratio of the m/z, retention time and
intensity components of the plot

\item[\code{...}] arguments passed to \code{\LinkA{profRange}{profRange}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The rgl package is still in development and imposes some limitations
on the output format. A bug in the axis label code means that the
axis labels only go from 0 to the aspect ratio constant of that
axis. Additionally the axes are not labeled with what they are.

It is important to only plot a small portion of the profile matrix.
Large portions can quickly overwhelm your CPU and memory.
\end{Details}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{plotSurf(object, log = FALSE, aspect = c(1, 1, .5), ...)}

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

