\Header{plot.som}{Visualizing a SOM}
\keyword{hplot}{plot.som}
\begin{Description}\relax
Plot the SOM in a 2-dim map with means and sd bars.\end{Description}
\begin{Usage}
\begin{verbatim}
plot(x, sdbar=1, ylim=c(-5, 5), color=TRUE,
ntik=3, yadj=0.1, xlab="", ylab="", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a som object 
\item[\code{sdbar}] the length of sdbar in sd, no sdbar if sdbar=0 
\item[\code{ylim}] the range of y axies in each cell of the map 
\item[\code{color}] whether or not use color plotting 
\item[\code{ntik}] the number of tiks of the vertical axis 
\item[\code{yadj}] the proportion used to put the number of obs 
\item[\code{xlab}] x label 
\item[\code{ylab}] y label 
\item[\code{...}] other options to plot 
\end{ldescription}
\end{Arguments}
\begin{Note}\relax
This function is not cleanly written. The original purpose was to
mimic what GENECLUSTER does. The ylim is hardcoded so that only
standardized data could be properly plotted.

There are visualization methods like umat and sammon in SOM\_PAK3.1,
but not implemented here.\end{Note}
\begin{Author}\relax
Jun Yan <jyan@stat.wisc.edu>\end{Author}
\begin{Examples}
\begin{ExampleCode}
foo <- som(matrix(rnorm(1000), 250), 3, 5)
plot(foo, ylim=c(-1, 1))
\end{ExampleCode}
\end{Examples}

