\name{gseaPlots}
\alias{gseaPlots}
\title{
Plot GSEA results for one gene set
}
\description{
This function takes in the output of gseaScores and the named vector 
of phenotypes, and plots the positions of genes of the gene set in 
the ranked phenotype vector and the location of the enrichment score.  
}
\usage{
gseaPlots(runningScore, enrichmentScore, positions, geneList)
}
\arguments{
  \item{runningScore}{
a single numeric value specifying the enrichment score returned from the
function "gseaScores"
}
  \item{enrichmentScore}{
a numeric vector of running sum scores (only in mode "graph")
}
  \item{positions}{
a numeric vector specifying positions in the ranked phenotype vector 
of the genes in the gene set (only in mode "graph")
}
  \item{geneList}{
a numeric or integer vector of phenotypes in descending or ascending
order with elements named by their EntrezIds (no duplicates nor NA values)
}
}
\references{
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L.,
Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander,
E. S. & Mesirov, J. P. (2005)  \emph{Gene set enrichment analysis: A
knowledge-based approach for interpreting genome-wide expression profiles.}
Proc. Natl. Acad. Sci. USA 102, 15545-15550.
}
\author{
Camille Terfve, Xin Wang
}
\seealso{
\code{\link[HTSanalyzeR:plotGSEA]{plotGSEA}}, \code{\link[HTSanalyzeR:viewGSEA]{viewGSEA}}
}
\examples{
\dontrun{
library(org.Dm.eg.db)
library(KEGG.db)
##load phenotype vector (see the vignette for details about the
##preprocessing of this data set)
data("KcViab_Data4Enrich")
DM_KEGG <- KeggGeneSets(species="Dm")
GSCscores <- gseaScores(geneList=KcViab_Data4Enrich, geneSet=DM_KEGG[[1]],
exponent=1, mode="graph")
gseaPlots(runningScore=GSCscores$runningScore, enrichmentScore=
GSCscores$enrichmentScore, positions=GSCscores$positions,
geneList=KcViab_Data4Enrich)
}
}