[BioC] using pathview about hsa01100

[Luo Weijun]

Hi Weiwei,
I don’t think pathview can work with this diagram. It is not a real KEGG pathway graph.
However, I notice that you can do User data mapping on the web page:
http://www.genome.jp/kegg-bin/show_pathway?hsa01100
Of course, you have to generate the input file with colors manually. And there will no color key etc. It may not look that neat even if you finally make it. You see, the raw graph already has a lot of different colors, and the nodes look too small compared to the whole graph.

My suggestion would be have a pathway analysis done on your data using GAGE or another method, and visualize the perturbed pathways separately using pathview.
Weijun

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On Thu, 8/1/13, Ed <edforum at gmail.com> wrote:

 Subject: using pathview about hsa01100
 To: "bioconductor at r-project.org" <bioconductor at r-project.org>, "Luo Weijun
 Date: Thursday, August 1, 2013, 5:52 PM

 Hi Weijun,
 In terms of the topmost metabolic
 pathway "hsa01100", I would like to highlight some
 enzymes on this pathway, however, it seems the
 "circles" on the plot are metabolites instead of
 enzymes. The enzymes are the "edges" on the
 plot.

 Do you know how to deal with this
 question?
 Alternatively, if there is a way to
 highlight the circles instead of edges, that's also
 fine. But is there a way to find the "circles" for
 the "edge"?

 Thanks,
 Weiwei