\HeaderA{plot.stamFit}{Plots for StAM Model Fit}{plot.stamFit}
\keyword{hplot}{plot.stamFit}
\begin{Description}\relax
Overall alpha vs. delta plot as well as nodewise scatter plots on 
performance/redundancy and specificity/sensitivity.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'stamFit':
plot(x, outfile = NULL, aclass = NULL, main = NULL,
             which = 0, res = 72, ps = FALSE, pointsize = 12, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] the object of type stamFit for which the plots are to be drawn
\item[\code{outfile}] name of output file if postscript or PNG graphics is to be generated. 
The extension of the file is chosen automatically according to the \code{ps} 
argument. The filename is also augmented by suffixses to distinguish the plots 
generated. If no outfile is specified, an interactive plot is attempted
\item[\code{aclass}] the name of the phenotype class of interest, usually the disease class
\item[\code{which}] choose the plot to be generated. 1:alpha vs. delta, 2:nodewise evaluation, 
0:both plots in interactive mode, non otherwise.
\item[\code{main}] the main title of the plot, generated automatically if left blank
\item[\code{res}] resolution in points per inch
\item[\code{ps}] if set to TRUE postscript output is generated
\item[\code{pointsize}] the standard fontsize
\item[\code{...}] additional arguments to be passed to plot
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If several values for alpha are provided to stam.fit plot.stamFit generates a compound 
score vs. shrinkage level plot. For each alpha one line is drawn and the best shrinkage
(where the minimum is achieved) is marked. In a second pane of the same plot alpha is 
plotted vs. these best shrinkage levels.

Additionally nodewise scatter plots comparing performance vs. 
redundancy and sensitivity vs. specificity are generated.
\end{Details}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stam.fit}{stam.fit}}
\end{SeeAlso}

