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

[Luo Weijun]

Weiwei,
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:

library(pathview)
xml.file="hsa01100.xml"
gR1=pathview:::parseKGML2Graph2(xml.file, genesOnly=FALSE, expand=FALSE, split.group=FALSE)
node.data=node.info(gR1)
edge.names=names(edgeData(gR1))

head(node.data$kegg.names)
head(edge.names)

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

--------------------------------------------
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
 idea?

 Thanks,
 Weiwei



 On Fri, Aug 16, 2013 at

 wrote:

 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.

 Weijun



 --------------------------------------------

 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.



  Thanks,

  weiwei







  On Thu, Aug 15, 2013



  wrote:



  Hi

  Weiwei,



  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:





  http://pathview.r-forge.r-project.org/#fig-5







  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.





  Weijun







  library(pathview)



  sim.cpd.data=sim.mol.data(mol.type="cpd",

  nmol=3000)



  data(cpd.simtypes)



  #~30 min



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

  "01100",



      species = "hsa", out.suffix =

  "sim.cpd", kegg.native = T)



  #~15 sec



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

  "01100",



      species = "hsa", out.suffix =

  "sim.cpd.2layer ", kegg.native = T, same.layer
 =

  F)







  --------------------------------------------



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

  wrote:







   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



   hsa01100?



   thanks,



   weiwei











   On Fri, Aug 2, 2013 at







   wrote:







   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















   --------------------------------------------







   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>,















    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