\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(abf1)
# fit the anova model
## Not run: 
fit.fix = fitmaanova(abf1,formula = ~Strain)
# test Strain effect 
test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
# pick significant genes - pick the genes selected by Fs test
idx <- volcano(test.fix)$idx.Fs
geneprofile(fit.fix, "Strain", idx)
## End(Not run)
\end{ExampleCode}
\end{Examples}

