[BioC] Pathview published in Bioinformatics

[Luo Weijun]

A little more info. You
may download the KGML data file for Propanoate metabolism pathway. Gene nodes
correspond to node entries with type="gene", while white nodes
correspond to entries with type="ortholog", ortholog genes which are
not mapped for a particular KEGG species. 
These ortholog gene
nodes are still show are in both KEGG and Graphviz view, except no gene data
can be mapped when calling pathview function with species = "hsa" (or
other KEGG species). However, gene data can still be mapped to these nodes when
species = "ko". This is relevant for ortholog gene data or
metagenomic data.
HTH.


----- Original Message -----
From: Luo Weijun <luo_weijun at yahoo.com>
To: Ed <edforum at gmail.com>
Cc: BioC Help <bioconductor at r-project.org>
Sent: Thursday, June 27, 2013 6:32 PM
Subject: Re: [BioC] Pathview published in Bioinformatics

Yes, you can replace
get gene symbols instead of EC numbers by setting kegg.native = T, same.layer =
F for KEGG view. However, only those enzyme nodes/genes which are present in
the KGML data file. These nodes are marked in green in original KEGG graph for
particular species, for example Propanoate
metabolism - Homo sapiens:
http://www.genome.jp/kegg-bin/show_pathway?map=hsa00640
In fact for Graphviz
view (kegg.native = F), the pathway graph are also limited to genes which are
presented in KGML data file. Hence you may see some inconsistence for metabolic
pathway graphs between KEGG view and Graphviz view. Unfortunately, there is
little we are limited by the KGML source data files.


________________________________
From: Ed <edforum at gmail.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> wrote:

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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>>
>
>
>