\HeaderA{plotP}{SPIA two-way evidence plot}{plotP}
\keyword{nonparametric}{plotP}
\keyword{methods}{plotP}
\begin{Description}\relax
Plots each pathway as a point, using the over-representation p-value, pNDE, and perturbations accumulation p-value,
pPERT, as coordinates.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotP(x,threshold=0.05)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] A data frame produced by \code{\LinkA{spia}{spia}} function.
\item[\code{threshold}] A numerical value between 0 and 1 to be used as significance threshold in inferring pathway significance.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
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.
\end{Details}
\begin{Value}
This function does not return any value. It only generates a plot.
\end{Value}
\begin{Author}\relax
Adi Laurentiu Tarca \textless{}atarca@med.wayne.edu\textgreater{}, Purvesh Khatri, Sorin Draghici
\end{Author}
\begin{References}\relax
Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for 
Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82. \\
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{spia}{spia}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# 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)
\end{ExampleCode}
\end{Examples}

