\HeaderA{plotrt-methods}{Plot retention time deviation profiles}{plotrt.Rdash.methods}
\aliasA{plotrt}{plotrt-methods}{plotrt}
\aliasA{plotrt,xcmsSet-method}{plotrt-methods}{plotrt,xcmsSet.Rdash.method}
\keyword{methods}{plotrt-methods}
\keyword{hplot}{plotrt-methods}
\begin{Description}\relax
Use corrected retention times for each sample to calculate retention
time deviation profiles and plot each on the same graph.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{col}] vector of colors for plotting each sample
\item[\code{ty}] vector of line and point types for plotting each sample
\item[\code{leg}] logical plot legend with sample labels
\item[\code{densplit}] logical, also plot peak overall peak density
\end{ldescription}
\end{Arguments}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{plotrt(object, col = NULL, ty = NULL, leg = TRUE, 
               densplit = FALSE)}

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\code{\LinkA{retcor}{retcor}}
\end{SeeAlso}

