\HeaderA{trad.scatter.plot}{Does a Traditional Scatter Plot of Expression Data}{trad.scatter.plot}
\keyword{misc}{trad.scatter.plot}
\begin{Description}\relax
Plots expression data as a scatter plot with optional fold-change lines
\end{Description}
\begin{Usage}
\begin{verbatim}
trad.scatter.plot(x, y, add = FALSE, fc.lines = log2(c(2, 4, 6, 8)), draw.fc.lines = TRUE, draw.fc.line.labels = TRUE, fc.line.col = "lightgrey", pch = 20,xlim=NULL,ylim=NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] x coords 
\item[\code{y}] y coords 
\item[\code{add}] add this data to an existing graph 
\item[\code{fc.lines}] Vector of intervals at which to draw fold-change lines 
\item[\code{draw.fc.lines}] Draw fold change lines? 
\item[\code{draw.fc.line.labels}] Label the fold change lines with the fold changes they represent? 
\item[\code{fc.line.col}] The colour to draw fold change lines 
\item[\code{pch}] Plotting character to use for the scatter data (see \code{plot} for more details) 
\item[\code{xlim}] Range for the xaxis 
\item[\code{ylim}] Range for the yaxis 
\item[\code{...}] Additional parameters to pass through to the underlying \code{plot} function 
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{References}\relax
http://bioinformatics.picr.man.ac.uk/
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{plot}{plot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  ## Not run: 
    trad.scatter.plot(exprs(eset.rma)[,1],exprs(eset.rma)[,4])
  
## End(Not run)
\end{ExampleCode}
\end{Examples}