\HeaderA{plotGenePair}{Scatter plots for pair of genes}{plotGenePair}
\keyword{classes}{plotGenePair}
\begin{Description}\relax
This function displays scatter plots for pair of genes that presented
altered correlation values in Relevance Network analysis.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotGenePair(obj, gene1, gene2, posL=NULL, rCor=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{obj}] object of class \code{\LinkA{maigesRelNetM}{maigesRelNetM}}.
\item[\code{gene1}] character string giving the first gene identification.
\item[\code{gene2}] character string giving the first gene identification.
\item[\code{posL}] numerical vector of length 2, specifying the x and y
position of the legend.
\item[\code{rCor}] logical specifying if the correlation are robust
(calculated by the function \code{\LinkA{robustCorr}{robustCorr}}. Defaults to TRUE.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function only picks the result of the \code{\LinkA{relNetworkM}{relNetworkM}}
and display scatter plots for a pair of genes giving the regression
lines and the correlation values for the two biological groups tested.
\end{Details}
\begin{Value}
This function don't return any object.
\end{Value}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{maigesRelNetM}{maigesRelNetM}}, \code{\LinkA{robustCorr}{robustCorr}}, \code{\LinkA{relNetworkM}{relNetworkM}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Constructing the relevance network for sample
## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
  samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
  type="Rpearson")

## As the sample size is small, because we used a small fraction of the
## genes from the original dataset, this isn't so reliable.
plotGenePair(gastro.net, "KLK13", "EVPL")
\end{ExampleCode}
\end{Examples}

