\HeaderA{stam.writeHTML}{Write StAM Output in HTML}{stam.writeHTML}
\keyword{hplot}{stam.writeHTML}
\begin{Description}\relax
Write HTML output for various pieces of a structured analysis of microarray data for 
further interactive exploration.
\end{Description}
\begin{Usage}
\begin{verbatim}
stam.writeHTML(x, title = NULL, align = "left", 
               outfile = "index.html", nonodes = FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] the piece of the analysis for which HTML is to be generated. It may be of any 
of the following classes: \code{stamNode}, \code{stamNet}, \code{stamCV}, 
\code{stamFit}, \code{stamPrediction} or \code{stamEval}
\item[\code{title}] the title to be used on the generated main page. A default is generated 
according to a few important parameters of \code{x}
\item[\code{align}] alignment of the tatle (left, right, center)
\item[\code{outfile}] the file where to store the generated HTML code unless \code{x} is of 
class \code{stamEval}. In the latter case, \code{outfile} is a directory where the 
the collection of files is stored. 
\item[\code{nonodes}] whether to generate (possibly lengthy) output for all nodes
\item[\code{...}] further arguments passed to \code{writeHTML} calls.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Use this function to generate HTML pages for further investigation of StAM results. The 
pages are interlinked and contain links to external resources such as the Gene Ontology 
and the Affymetrix website. Clickable maps are generated for the illustration of the 
model fit as well as the molecular symptoms image.
\end{Details}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
data(golubTrain.cv)
data(golubTrain.fit)

stam.writeHTML(golubTrain.cv)
stam.writeHTML(golubTrain.fit, nonodes=TRUE)
## End(Not run)\end{ExampleCode}
\end{Examples}

