[BioC] Pathview for global and overview maps Re: using pathview about hsa01100

Luo Weijun luo_weijun at yahoo.com
Fri Aug 16 23:26:03 CEST 2013

I don’t think pathview will do that. You will need to parse the xml manually to be able to do that.Pathview’s integrated parser works with normal pathways, where enzymes and genes are defined as rectangle nodes. Here they are edges. 
Again, for these global maps, only working with compound/metabolite nodes are fine, but not so when touching other record types.

On Thu, 8/15/13, Nick <edforum at gmail.com> wrote:

 Subject: Re: Pathview for global and overview maps Re: using pathview about hsa01100

 Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
 Date: Thursday, August 15, 2013, 10:11 PM

 Hi Weijun,
 It is one step away from what I want. However, I
 am wondering if, for example, I have an enzyme and would
 like to highlight its substrate and product, is it possible
 to do so? For example NME3 in pyrimidine metabolic pathway,
 I want to highlight its substrate and product in such global
 map like hsa01100.


 On Thu, Aug 15, 2013



 If you just want to the highlight the metabolite/compound
 nodes (without dealing with the enzymes etc) in such Global
 and overview maps like hsa01100, you may still use pathview
 like for individual metabolic pathways. You may see an
 example output here:


 You will notice that the round compound nodes are amplified
 for better view of the data. Below is the code I used. It
 works, but takes a long time (30 min for me on my desktop).
 The time is needed because there are so many nodes to be
 edited pixel by peixel. Option same.layer = F would speed up
 the process over 100 times, although the graph looks a
 little different as expected. HTH.





 #~30 min

 pv.out <- pathview(cpd.data = sim.cpd.data, pathway.id =

     species = "hsa", out.suffix =
 "sim.cpd", kegg.native = T)

 #~15 sec

 pv.out <- pathview(cpd.data = sim.cpd.data, pathway.id =

     species = "hsa", out.suffix =
 "sim.cpd.2layer ", kegg.native = T, same.layer =


 On Wed, 8/14/13, Ed <edforum at gmail.com>

  Subject: Re: using pathview about hsa01100

  Date: Wednesday, August 14, 2013, 3:13 PM

  Hi Weijun,

  I mean if I can highlight the chemical nodes from




  On Fri, Aug 2, 2013 at


  Hi Weiwei,

  I don’t think pathview can work with this diagram. It

  not a real KEGG pathway graph.

  However, I notice that you can do User data mapping on

  web page:


  Of course, you have to generate the input file with

  manually. And there will no color key etc. It may not

  that neat even if you finally make it. You see, the raw

  graph already has a lot of different colors, and the

  look too small compared to the whole graph.

  My suggestion would be have a pathway analysis done on

  data using GAGE or another method, and visualize the

  perturbed pathways separately using pathview.



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


   Subject: using pathview about hsa01100

   To: "bioconductor at r-project.org"

  <bioconductor at r-project.org>,

   Date: Thursday, August 1, 2013, 5:52 PM

   Hi Weijun,

   In terms of the topmost metabolic

   pathway "hsa01100", I would like to highlight


   enzymes on this pathway, however, it seems the

   "circles" on the plot are metabolites instead


   enzymes. The enzymes are the "edges" on the


   Do you know how to deal with this


   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


   the "edge"?



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