\HeaderA{getComponents}{KEGG pathway information}{getComponents}
\aliasA{color.pathway.by.elements}{getComponents}{color.pathway.by.elements}
\aliasA{get.elements.by.pathway}{getComponents}{get.elements.by.pathway}
\keyword{file}{getComponents}
\begin{Description}\relax
1. get connected pathway components; 2. get all elements of a given pathway; 3. color certain elements in a pathway.
\end{Description}
\begin{Usage}
\begin{verbatim}
getComponents(pathway.id)

get.elements.by.pathway(pathway.id)

color.pathway.by.elements(pathway.id, elements)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pathway.id}] KEGG pathway ID, e.g. "path:hsa04012"
\item[\code{elements}] KEGG element IDs: character vector of numbers
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
All functions use the KEGG SOAP service.
\end{Details}
\begin{Value}
getComponents: a list with the entries
\begin{ldescription}
\item[\code{geneIDs}] Entrez gene IDs mapping to each pathway component
\item[\code{elemIDs}] KEGG element IDs mapping to each pathway component
\end{ldescription}


get.elements.by.pathway: list, see \textless{}URL http://www.genome.jp/kegg/soap/doc/keggapi\_manual.html\textgreater{} for details

color.pathway.by.elements: an URL of a colored gif file, see \textless{}URL http://www.genome.jp/kegg/soap/doc/keggapi\_manual.html\textgreater{} for details
\end{Value}
\begin{Author}\relax
Holger Froehlich
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
  comp = getComponents("path:hsa04020") # get all connected components
  color.pathway.by.elements("path:hsa04020", comp$elemIDs[[1]]) # mark first component
## End(Not run)
\end{ExampleCode}
\end{Examples}

