\HeaderA{geneprofile}{Expression plot for selected genes}{geneprofile}
\keyword{hplot}{geneprofile}
\begin{Description}\relax
This function generate a plot with many lines. Each line represents
a gene. The y-axis is the estimated expression level for the given
factor from ANOVA model. The x-axis is for the levels of the
give factor, e.g.,  different strains.
\end{Description}
\begin{Usage}
\begin{verbatim}
geneprofile(anovaobj, term, geneidx,
            col="blue", type="b", ylim, xlab, ylab, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{anovaobj}] An object of class \code{maanova}. It should be the
result from \code{\LinkA{fitmaanova}{fitmaanova}}.
\item[\code{term}] The terms to be plotted.
\item[\code{geneidx}] The index of genes to be plotted.
\item[\code{col}] The color to be used in plot.
\item[\code{type}] The line type.
\item[\code{ylim}] Y-axis limit.
\item[\code{xlab}] X-axis label.
\item[\code{ylab}] Y-axis label.
\item[\code{...}] Other parameters to be passed to
\code{\LinkA{plot}{plot}}.
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Hao Wu
\end{Author}
\begin{Examples}
\begin{ExampleCode}
# load in data
data(paigen)
# make data object with rep 2
paigen <- createData(paigen.raw, 2)
# make an additive model
model.add.fix <- makeModel(data=paigen, formula=~Dye+Array+Strain+Diet)
# fit ANOVA model
anova.add <- fitmaanova(paigen, model.add.fix)
# test strain effect
## Not run: test.Strain.fix <- matest(paigen, model.add.fix, term="Strain", n.perm=100)
# volcano plot
idx <- volcano(test.Strain.fix)

# do gene profile for the selected genes
geneprofile(anova.add, "Strain", idx$idx.all)## End(Not run)
\end{ExampleCode}
\end{Examples}

