\HeaderA{Plot.all}{Combined visualization of sequential decomposition and influence of single genes on the GlobalAncova statistic}{Plot.all}
\keyword{hplot}{Plot.all}
\begin{Description}\relax
Plot that combines \code{\LinkA{Plot.genes}{Plot.genes}} and \code{\LinkA{Plot.sequential}{Plot.sequential}} into one graphic.
\end{Description}
\begin{Usage}
\begin{verbatim}
Plot.all(xx, formula, model.dat = NULL, test.genes = NULL, name.geneset = "")\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{xx}] Matrix of gene expression data, where columns correspond to samples
and rows to genes. The data should be properly normalized beforehand
(and log- or otherwise transformed). Missing values are not allowed.
Gene and sample names can be included as the row and column
names of \code{xx}.
\item[\code{formula}] Model formula for the linear model.
\item[\code{model.dat}] Data frame that contains all the variable information for each sample.
\item[\code{test.genes}] Vector of gene names or gene indices specifying a gene set.
\item[\code{name.geneset}] Name of the plotted geneset.
\end{ldescription}
\end{Arguments}
\begin{Note}\relax
This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.
\end{Note}
\begin{Author}\relax
Ramona Scheufele \email{ramona.scheufele@charite.de} \\
Reinhard Meister \email{meister@tfh-berlin.de}\\
Manuela Hummel \email{hummel@ibe.med.uni-muenchen.de} \\
Urlich Mansmann \email{mansmann@ibe.med.uni-muenchen.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{Plot.genes}{Plot.genes}}, \code{\LinkA{Plot.sequential}{Plot.sequential}}, \code{\LinkA{GlobalAncova.decomp}{GlobalAncova.decomp}}, \code{\LinkA{GlobalAncova}{GlobalAncova}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(vantVeer)
data(phenodata)
data(pathways)

Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway")
\end{ExampleCode}
\end{Examples}

