[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
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
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