[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.
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
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