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

Luo Weijun luo_weijun at yahoo.com
Mon Aug 19 21:40:01 CEST 2013

Although pathview main function does not do exactly what you want. You may still use pathview’s internal parser function, parseKGML2Graph2, which parse reaction records into edges/relations. You can do something like:

gR1=pathview:::parseKGML2Graph2(xml.file, genesOnly=FALSE, expand=FALSE, split.group=FALSE)


>From there you can sort out what are the compound nodes (products/substrates) connected to your enzyme nodes.

On Fri, 8/16/13, 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: Friday, August 16, 2013, 5:47 PM

 Yes. I agree.
 Actually I just want to touch the nodes
 (compounds) but I need to find how to know the ids (used on
 that map) for the substrate/product of an enzyme. Any


 On Fri, Aug 16, 2013 at


 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

 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>

  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

  to do so? For example NME3 in pyrimidine metabolic

  I want to highlight its substrate and product in such

  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

  and overview maps like hsa01100, you may still use

  like for individual metabolic pathways. You may see an

  example output here:


  You will notice that the round compound nodes are

  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

  The time is needed because there are so many nodes to be

  edited pixel by peixel. Option same.layer = F would speed

  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


    enzymes on this pathway, however, it seems the

    "circles" on the plot are metabolites


    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

    fine. But is there a way to find the



    the "edge"?



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