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 at 10:01 PM, Luo Weijun <luo_weijun@yahoo.com> 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@gmail.com> wrote:
>
>  Subject: Re: using pathview about hsa01100
>  To: "Luo Weijun" <luo_weijun@yahoo.com>
>  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
>  1:58 PM, Luo Weijun <luo_weijun@yahoo.com>
>  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@gmail.com>
>  wrote:
>
>
>
>   Subject: using pathview about hsa01100
>
>   To: "bioconductor@r-project.org"
>  <bioconductor@r-project.org>,
>  "Luo Weijun" <luo_weijun@yahoo.com>
>
>
>   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
>
>
>
>
>
>
>
>
>
>
>

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