\HeaderA{root.mvaplot}{ROOT M vs A Plot}{root.mvaplot}
\keyword{device}{root.mvaplot}
\begin{Description}\relax
Creates a ROOT M vs A plot for a ROOT tree.
\end{Description}
\begin{Usage}
\begin{verbatim}
root.mvaplot(x, treename1 = character(0), treename2 = character(0),logbase = "log2", option = "P", canvasname = "MvAPlot", save.as = "", w = 540, h = 540)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{ExprTreeSet}{ExprTreeSet}} or \code{\LinkA{DataTreeSet}{DataTreeSet}}.
\item[\code{treename1}] name of first tree, must be present in \code{rootfile} of object \code{x}.
\item[\code{treename2}] name of second tree, must be present in \code{rootfile} of object \code{x}.
\item[\code{logbase}] usually \dQuote{log2}, or \dQuote{0}, determines if leaf data should be converted to log.
\item[\code{option}] ROOT TGraph::PaintGraph option, usually one of \dQuote{P}, \dQuote{*}.
\item[\code{canvasname}] name of ROOT canvas
\item[\code{save.as}] gaphics tye for saving canvas, one of \dQuote{ps}, \dQuote{eps}, \dQuote{pdf},
\dQuote{jpg}, \dQuote{gif}, \dQuote{png}, \dQuote{tiff}
\item[\code{w}] the width of the canvas in pixels.
\item[\code{h}] the height of the canvas in pixels.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Creates a ROOT M vs A plot for trees \code{treename1} and \code{treename2} present in \code{rootfile}.

By selecting menu \dQuote{File->Save->canvasname.xxx} you can save the figure as e.g. *gif, *.jpg, *.pdf, *.ps or even as C++ macro.

Alternatively, you can save the plot by setting \code{save.as}. However, this will close the
canvas immediately after opening it.
\end{Details}
\begin{Note}\relax
Always select menu item \dQuote{Quit ROOT} from menu \dQuote{File} to close the ROOT canvas,
otherwise you are in the CINT C/C++ interpreter from \code{\LinkA{ROOT}{ROOT}}. To exit CINT,
you need to type \dQuote{.q}.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{root.graph1D}{root.graph1D}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

# compute RMA
data.rma <- rma(data.test3,"Test3RMA",tmpdir="",background="pmonly",normalize=TRUE)

root.mvaplot(data.rma, "TestA1.mdp", "TestB1.mdp")
## End(Not run)
\end{ExampleCode}
\end{Examples}

