\HeaderA{volcanoplot-methods}{Volcano Plot}{volcanoplot.Rdash.methods}
\aliasA{volcanoplot}{volcanoplot-methods}{volcanoplot}
\keyword{methods}{volcanoplot-methods}
\begin{Description}\relax
Produce a scatter plot of fold-change values vs p-values, called volcano plot.

\emph{Usage}

\code{
volcanoplot(x,
            labels      = "",
            p.value     = "pval",
            mask        = FALSE,
            show.cutoff = TRUE,
            cex.text    = 0.7,
            col.text    = "blue",
            col.cutoff  = "grey",
            xlim        = NULL,
            xlab        = "Log2(Fold-Change)",
            ylab        = "-Log10(P-Value)",
            pch         = '.',
            ...) 
}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}}.
\item[\code{labels}] optional transcript labels to be drawn at plotting points.
\item[\code{p.value}] type of p-value, 'pval' for p-value, 'padj' for adjusted p-value, or 'pcha' for p-chance.
\item[\code{mask}] logical, if \code{TRUE} draw only points for transcripts satisfying the univariate test.
\item[\code{show.cutoff}] logical, if \code{TRUE} draw lines indicating cutoff.
\item[\code{cex.text}] magnification to be used for optional \code{labels}.
\item[\code{col.text}] color to be used for optional \code{labels}.
\item[\code{col.cutoff}] color to be used for lines indicating cutoff, if \code{show.cutoff=TRUE}.
\item[\code{xlim}] optional range for the plotted fold-change values.
\item[\code{xlab}] label of x-axis.
\item[\code{ylab}] label of y-axis.
\item[\code{pch}] either an integer specifying a symbol or a single character to be used as the default in plotting points.
\item[\code{...}] optional arguments to be passed to \code{plot}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Produces a volcano plot for slot \code{data} for an object of class \code{\LinkA{AnalysisTreeSet}{AnalysisTreeSet}}.

It is possible to label the points of the volcano plot, whereby the following
\code{labels} parameters are valid:
\Tabular{lll}{
& \code{fUnitName}:& unit name (probeset ID). \\
& \code{fName}:& gene name. \\
& \code{fSymbol}:& gene symbol. \\
& \code{fChromosome}:& chromosome. \\
& \code{fCytoBand}:& cytoband.
}
\end{Details}
\begin{Author}\relax
Christian Stratowa
\end{Author}

