\name{plotRP}
\alias{plotRP}
\title{Graphical Display of the Rank Product/Sum analysis}
\description{  
     Plot a graphical display of the estimated pfp vs 
     number of identified genes}

\usage{
     plotRP(x, cutoff=NULL)}

\arguments{
     \item{x}{the value returned by function RP, 
           RPadvance or RSadvance }
     
     \item{cutoff}{threshold in pfp used to select genes}
}  
     
\value{
     A graphical display of the estimated pfp vs number of 
     identified genes, which is also the gene rank of its 
     original rank product/sum across all comparison. If cutoff 
     is sepcified, a horizontal line will be plotted on the 
     graphic to indicate the positon of the cutoff point, and 
     all genes identified will be marked red.
     
     Two plots will be displayed, one for the identification of 
      up-regulated genes in class 2, one for the identification of 
      down-regulated genes in class 2

}

\author{Fangxin Hong \email{fhong@salk.edu}}

\seealso{
    \code{\link{topGene}}   \code{\link{RP}}  
    \code{\link{RPadvance}} \code{\link{RSadvance}}
}

\examples{
     
      # Load the data of Golub et al. (1999). data(golub) 
      #contains a 3051x38 gene expression
      # matrix called golub, a vector of length called golub.cl 
      #that consists of the 38 class labels,
      # and a matrix called golub.gnames whose third column contains the gene names.
      data(golub)
 
      #use a subset of data as example, apply the rank product method
      subset <- c(1:4,28:30)
      #Setting rand=123, to make the results reproducible,

      #identify genes that are up-regulated in class 2 
      #(class label =1)
      RP.out <- RP(golub[,subset],golub.cl[subset], rand=123)
      
      #plot the results
      plotRP(RP.out,cutoff=0.05)
      
}
\keyword{htest}