Can I use gene symbol but keep a native KEGG view? I mean, I just want to
replace the EC code with gene symbol without changing the layout or view of
KEGG pathway?

Thanks,

weiwei



On Thu, Aug 29, 2013 at 11:27 AM, Luo Weijun <luo_weijun@yahoo.com> wrote:

> 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.
> Weijun
>
> --------------------------------------------
> On Tue, 8/27/13, Nick <edforum@gmail.com> wrote:
>
>  Subject: Change enzyme code (EC) into gene symbol
>  To: "Luo Weijun" <luo_weijun@yahoo.com>
>  Cc: "BioC Help" <bioconductor@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?
>  thanks,
>
>  Weiwei
>
>

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