\HeaderA{sam.plot2}{SAM Plot}{sam.plot2}
\aliasA{plotArguments}{sam.plot2}{plotArguments}
\keyword{hplot}{sam.plot2}
\begin{Description}\relax
Generates a SAM plot for a specified value of Delta.
\end{Description}
\begin{Usage}
\begin{verbatim}
  sam.plot2(object, delta, pos.stats = NULL, sig.col = 3, xlim = NULL, 
        ylim = NULL, main = NULL, xlab = NULL, ylab = NULL, pty = "s", 
        lab = c(10, 10, 7), pch = NULL, sig.cex = 1, ...)
     
  plotArguments(pos.stats = NULL, sig.col = 3, xlim = NULL, ylim = NULL,
        main = NULL, xlab = NULL, ylab = NULL, pty = "s", lab = c(10, 10, 7),
        pch = NULL, sig.cex = 1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] an object of class SAM
\item[\code{delta}] a numeric value specifying the value of \eqn{\Delta}{Delta}
for which the SAM plot should be generated
\item[\code{pos.stats}] an integer between 0 and 2. If \code{pos.stats=1}, general
information as the number of significant genes and the estimated FDR for
the specified value of \code{delta} will be plotted in the upper left corner
of the plot. If \code{pos.stats=2}, these information will be plotted in
the lower right corner. If \code{pos.stats=0}, no information will be plotted.
By default, \code{pos.stats=1} if the expression score \eqn{d}{} can be both 
positive and negative, and \code{pos.stats=2} if \eqn{d}{} can only take positive
values
\item[\code{sig.col}] a specification of the color of the significant genes. If \code{sig.col}
has length 1, all the points corresponding to significant genes are marked in the
color specified by \code{sig.col}. If \code{length(sig.col)==2}, the down-regulated
genes, i.e. the genes with negative expression score \eqn{d}{}, are marked in the
color specified by \code{sig.col}[1], and the up-regulated genes, i.e. the genes
with positive \eqn{d}{}, are marked in the color specified by \code{sig.col}[2]. 
For a description of how colors are specified, see \code{?par}
\item[\code{xlim}] a numeric vector of length 2 specifying the x limits (minimum and maximum)
of the plot
\item[\code{ylim}] a numeric vector of length 2 specifying the y limits of the plot
\item[\code{main}] a character string naming the main title of the plot
\item[\code{xlab}] a character string naming the label of the x axis
\item[\code{ylab}] a character string naming the label of the y axis
\item[\code{pty}] a character specifying the type of plot region to be used. \code{"s"} (default)
generates a square plotting region, and \code{"m"} the maximal plotting region
\item[\code{lab}] a numeric vector of length 3 specifying the approximate number of tickmarks
on the x axis and on the y axis and the label size
\item[\code{pch}] either an integer specifying a symbol or a single character to be used as the
default in plotting points. For a description of how \code{pch} can be specified, see
\code{?par}
\item[\code{sig.cex}] a numerical value giving the amount by which the symbols of the significant
genes should be scaled relative to the default
\item[\code{...}] further graphical parameters. See \code{?plot.default} and \code{?par}
\end{ldescription}
\end{Arguments}
\begin{Value}
a SAM plot
\end{Value}
\begin{Note}\relax
SAM was deveoped by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!
\end{Note}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{References}\relax
Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays
applied to the ionizing radiation response. \emph{PNAS}, 98, 5116-5121.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}},\code{\LinkA{sam}{sam}},\code{\LinkA{sam.dstat}{sam.dstat}},\code{\LinkA{sam.wilc}{sam.wilc}},
\code{\LinkA{sam.snp}{sam.snp}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in multtest.
  library(multtest)
  data(golub)
  
  # Perform a SAM analysis for the two class unpaired case assuming
  # unequal variances.
  sam.out<-sam(golub,golub.cl,B=100,rand=123)
  
  # Generate a SAM plot for Delta = 2
  sam.plot2(sam.out,2)
  
  # Alternatively way of generating the same SAM plot
  plot(sam.out,2)
  
## End(Not run)\end{ExampleCode}
\end{Examples}