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

[Luo Weijun]

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