Entering edit mode
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)
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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
