\HeaderA{symbolsInteresting}{Useful for changing the look of pairs plots to emphasize
concordant or discordant genes}{symbolsInteresting}
\keyword{dplot}{symbolsInteresting}
\begin{Description}\relax
This function can be used to order genes in a matrix by the rank of a
statistic and provide different plotting symbols and colors for genes
that exceed a certain threshold of the ranking statistic.
\end{Description}
\begin{Usage}
\begin{verbatim}
symbolsInteresting(rankingStatistic, percentile = 0.9, colors = c("grey50", "royalblue"), symbols = c(".", "o"), size = c(3, 1), background = c("white", "grey70"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{rankingStatistic}] Any numerical vector 
\item[\code{percentile}] A percentile of the rankingStatistic -- above which
a gene would be classified as 'interesting'
\item[\code{colors}] character string of length 2: a color for genes not exceeding the
percentile and a color for genes exceeding the thresold
\item[\code{symbols}] two plotting symbols (numeric or character): symbol for
genes not exceeding percentile and symbol for genes exceeding percentile
\item[\code{size}] numeric vector of length 2: size of plotting symbol for genes not exceeding
percentile and size of plotting symbol for genes exceeding percentile 
\item[\code{background}] character vector of length 2: background color of
plotting symbols for gene not exceeding percentile and for genes
exceeding the percentile
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{order}] the order of the rankingStatistic
\item[\code{pch}] plotting symbols (same length as rankingStatistic)
\item[\code{col}] color of plotting symbols (same length as
rankingStatistic)
\item[\code{bg}] background color of plotting symbols (same length as
rankingStatistic)
\item[\code{cex}] size of plotting symbols (same length as
rankingStatistic)
\end{ldescription}
\end{Value}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{Examples}
\begin{ExampleCode}

  data(expressionSetList)
  data(xmcmc)
  bes <- bayesianEffectSize(xmcmc)
  postAvg <- posteriorAvg(xmcmc)
  op.conc <- symbolsInteresting(rankingStatistic=postAvg[, "concordant"])
  graphics:::pairs(bes[op.conc$order, ], pch=op.conc$pch, col=op.conc$col, 
                   bg=op.conc$bg, upper.panel=NULL, cex=op.conc$cex)  

\end{ExampleCode}
\end{Examples}

