[BioC] Change enzyme code (EC) into gene symbol

Luo Weijun luo_weijun at yahoo.com
Thu Aug 29 17:27:03 CEST 2013

Hi Weiwei,
Yes, you can get gene symbol instead of EC (or original KEGG node labels). If you want a native KEGG view, set kegg.native = T, same.layer = F when you call pathview function. Otherwise, simply set set kegg.native = F for a Graphviz view. 
Notice that you can only modify mappable gene nodes which are present in the KEGG xml file as gene nodes (rather than KO nodes) if you work with a particular species like human or hsa. You may have access to all Enzyme/gene nodes if you work with KO pathways (species="ko").
As example outputs, you may compare the gene symbols in Figure 1b and Figure 2 vs Figure 1a in the vignette. HTH.

On Tue, 8/27/13, Nick <edforum at gmail.com> wrote:

 Subject: Change enzyme code (EC) into gene symbol

 Cc: "BioC Help" <bioconductor at r-project.org>
 Date: Tuesday, August 27, 2013, 8:36 PM
 Hi there,
 I am wondering if you can change the ECs for each
 enzyme on the kegg graph like pyrimidine metabolism into
 gene symbol, for example?

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