\HeaderA{volcanoplot}{Volcano Plot}{volcanoplot}
\keyword{hplot}{volcanoplot}
\begin{Description}\relax
Creates a volcano plot of log-fold changes versus log-odds of differential expression.
\end{Description}
\begin{Usage}
\begin{verbatim}
volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, xlab="Log Fold Change", ylab="Log Odds", pch=16, cex=0.35, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fit}] an \code{MArrayLM} fitted linear model object
\item[\code{coef}] integer giving the coefficient
\item[\code{highlight}] number of top genes to be highlighted
\item[\code{names}] character vector giving text labels for the probes to be used in highlighting
\item[\code{xlab}] character string giving label for x-axis
\item[\code{ylab}] character string giving label for y-axis
\item[\code{pch}] vector or list of plotting characters. Default is integer code 16 which gives a solid circle.
\item[\code{cex}] numeric vector of plot symbol expansions. Default is 0.35.
\item[\code{...}] any other arguments are passed to \code{plot}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
A volcano plot is any plot which displays fold changes versus a measure of statistical significance of the change.
\end{Details}
\begin{Value}
A plot is created on the current graphics device.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of presentation plots following the fitting of a linear model in LIMMA is given in \LinkA{06.LinearModels}{06.LinearModels}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
#  See lmFit examples
\end{ExampleCode}
\end{Examples}

