Yes, you can replace
get gene symbols instead of EC numbers by setting kegg.native = T,
F for KEGG view. However, only those enzyme nodes/genes which are
the KGML data file. These nodes are marked in green in original KEGG
particular species, for example Propanoate
metabolism - Homo sapiens:
In fact for Graphviz
view (kegg.native = F), the pathway graph are also limited to genes
presented in KGML data file. Hence you may see some inconsistence for
pathway graphs between KEGG view and Graphviz view. Unfortunately,
little we are limited by the KGML source data files.
From: Ed <email@example.com>
To: Luo Weijun <luo_weijun at="" yahoo.com="">
Sent: Thursday, June 27, 2013 12:04 AM
Subject: Re: [BioC] Pathview published in Bioinformatics
so if I understand and tried correctly,
I cannot simply replace the EC in the graph (like Propanoate
metabolism) with gene symbol. If I need to do so, I need to set
kegg.native=F, which means it will change the graph structure of
Propanoate Metoblism. Am I right?
On Wed, Jun 26, 2013 at 1:03 PM, Luo Weijun <luo_weijun at="" yahoo.com="">
>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
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?
>On Tue, Jun 25, 2013 at 8:14 PM, Luo Weijun <luo_weijun at="" yahoo.com="">
>>The pathview package was recently published in
>>Pathview is an R/Bioconductor package for pathway based data
>>integration and visualization. It maps and renders a wide variety of
>>data on relevant pathway graphs.
>>The package is available through Bioconductor and R-Forge:
>>Please try it out and let me know if you have any
>>comments/suggestions. Thank you!
>>Bioconductor mailing list
>>Bioconductor at r-project.org
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