\name{plotP}
\alias{plotP}
\title{SPIA two-way evidence plot}
\description{
Plots each pathway as a point, using the over-representation p-value, pNDE, and perturbations accumulation p-value,
pPERT, as coordinates.
}
\usage{
plotP(x,threshold=0.05)
}
\arguments{
  \item{x}{A data frame produced by \code{\link{spia}} function.}
  \item{threshold}{A numerical value between 0 and 1 to be used as significance threshold in inferring pathway significance.}
}
  \details{In this plot each pathway is a point and the coordinates are the log of pNDE (using a hypergeometric model)
  and the p-value from perturbations, pPERT. The oblique lines in the plot show the significance 
  regions based on the combined evidence.}
\value{
 This function does not return any value. It only generates a plot.
}


\references{
Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for 
Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82. \cr

}
\author{Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Khatri, Sorin Draghici}

\seealso{\code{\link{spia}}}

\examples{
# Examples use colorectal cancer dataset
data(colorectalcancer)

# pathway analysis based on combined evidence of ORA and perturbations
# use nB=2000 or larger for more accurate results
res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",nB=200,plots=FALSE,verbose=TRUE,beta=NULL)

#Generate the evidence plot
plotP(res,threshold=0.1)
}

\keyword{nonparametric}% at least one, from doc/KEYWORDS
\keyword{methods}% __ONLY ONE__ keyword per line