Sure. Thanks. Actually I followed a couple of emails of a discussion of package called pathview but I changed the subject so it seemed an independent question to the forum and forgot to mention the background. On Tue, Aug 27, 2013 at 10:48 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi WeiWei, > > I don't know what graph you are talking about since you have not followed > the posting guide and given us a working example of what you are talking > about. But you can read it here for future reference: > > http://www.bioconductor.org/**help/mailing- list/posting-**guide/<http: www.bioconductor.org="" help="" mailing-list="" posting-guide=""/> > > But now I will guess and try to answer your question anyways. So assuming > that you have EC ids, you can definitely look up the gene symbols that map > to those. For example in human you can do it like this: > > ## load the organism package for humans > library(org.Hs.eg.db) > ## Now lets start by just grabbing some example EC IDs: > h <- head(keys(org.Hs.eg.db, keytype="ENZYME")) > h > ## not lets extract the corresponding symbols: > select(org.Hs.eg.db, keys=h, cols="SYMBOL", keytype="ENZYME") > > Hope this helps, > > > Marc > > > > On 08/27/2013 05:36 PM, Nick wrote: > >> 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 >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]

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 > > [[alternative HTML version deleted]]