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%\VignetteIndexEntry{pathRender overview}
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%\VignetteKeywords{pathway visualization, graphs}
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\documentclass[12pt]{article}

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\begin{document}
%\setkeys{Gin}{width=0.55\textwidth}
\title{pathRender: KEGG and Biocarta pathway visualization}
\author{VJ Carey (document)/Li Long (software)}
\maketitle

\section{Introduction}

Pathways are useful for organizing knowledge about
molecular biological processes.  Several major
catalogs of pathways are available, and this package
addresses the visualization of pathways from KEGG and
Biocarta.  Ultimately we want to be able to link
statistical data to pathway representations to aid
interpretation.  This package addresses only the
graph structures, annotation, and rendering of pathway
diagrams.  Much work remains to be done to 
harvest in a scalable and customizable way the information
provided on pathways.

\section{Quick illustrations}

\begin{figure}
<<do1,fig=TRUE,results=hide>>=
library(pathRender)
plot(G1 <- graphcMAP("p53pathway"))
G1
nodes(G1)[1:5]
@
\caption{A rendering of the p53 pathway according to Biocarta.}
\end{figure}

As of 9/15/2007 it is not clear why some of the symbols
are not translated to molecule or interaction terms.

\begin{figure}
\setkeys{Gin}{width=1.21\textwidth}
<<do2,fig=TRUE,height=12,width=12,results=hide>>=
plot(G2 <- graphcMAP("raspathway"))
@
\caption{A rendering of the Ras pathway according to Biocarta.
The height and width of the plotting surface are set to 12in each.}
\end{figure}

\end{document}