[BioC] Pathview published in Bioinformatics

[Luo Weijun]

Hi Nick,
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. As example outputs, you may compare the gene symbols
in Figure 1b and Figure 2 vs Figure 1a in the vignette. HTH.
Weijun

________________________________
From: Ed <edforum at gmail.com>
To: Luo Weijun <luo_weijun at yahoo.com> 
Sent: Tuesday, June 25, 2013 9:10 PM
Subject: Re: [BioC] Pathview published in Bioinformatics



Hi Dr. Luo,

It is a really good job!

I am just wondering if you can change the EC into gene symbol for the enzyme in KEGG pathway?

Thanks,

Nick





On Tue, Jun 25, 2013 at 8:14 PM, Luo Weijun <luo_weijun at yahoo.com> wrote:

BioC List,
>The pathview package was recently published in
>Bioinformatics:
>http://bioinformatics.oxfordjournals.org/content/early/2013/06/11/bioinformatics.btt285.full
> 
>Pathview is an R/Bioconductor package for pathway based data
>integration and visualization. It maps and renders a wide variety of biological
>data on relevant pathway graphs.
> 
>The package is available through Bioconductor and R-Forge:
>http://bioconductor.org/packages/release/bioc/html/pathview.html
>http://pathview.r-forge.r-project.org/
>Please try it out and let me know if you have any
>comments/suggestions. Thank you!
>Weijun Luo
>
>
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