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Question: Pathview for global and overview maps Re: using pathview about hsa01100
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gravatar for Luo Weijun
4.9 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k 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
ADD COMMENTlink modified 4.9 years ago by Ed230 • written 4.9 years ago by Luo Weijun1.4k
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gravatar for Ed
4.9 years ago by
Ed230
Ed230 wrote:
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 > > > > > > > > > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.9 years ago by Ed230
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
ADD REPLYlink written 4.9 years ago by Luo Weijun1.4k
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 5:26 PM, Luo Weijun <luo_weijun@yahoo.com> 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@gmail.com> wrote: > > Subject: Re: Pathview for global and overview maps Re: using pathview > about hsa01100 > To: "Luo Weijun" <luo_weijun@yahoo.com> > Cc: "bioconductor@r-project.org" <bioconductor@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 > 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 > > > > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.9 years ago by Ed230
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
ADD REPLYlink written 4.9 years ago by Luo Weijun1.4k
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