Hello,
>From a couple of interesting gene lists I have found KEGG pathways
which
contain genes from both lists. Does anyone know how to visualise
this?
I was thinking something along the lines of the KEGG pathway being
plotted and the genes from the two lists highlighted in different
colours.
I can cope with this not being done in bioconductor but would prefer
it
if the final image was exported as PDF. I have searched around
without
much luck ... it seems possible that KEGGgraph maybe able to do it but
it is not clear from vignette.
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
This e-mail message is confidential and for use by the
a...{{dropped:2}}
Daniel Brewer wrote:
> Hello,
>
> >From a couple of interesting gene lists I have found KEGG pathways
which
> contain genes from both lists. Does anyone know how to visualise
this?
> I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different
colours.
>
> I can cope with this not being done in bioconductor but would prefer
it
> if the final image was exported as PDF. I have searched around
without
> much luck ... it seems possible that KEGGgraph maybe able to do it
but
> it is not clear from vignette.
>
> Dan
>
>
Hi Daniel,
>From your post it is a little bit unclear to me exactly what you want
to
happen. KEGGgraph (which you mentioned), has a few vignettes that
might
help you. One of them is actually about plotting KEGG pathways. You
can
find those here:
http://www.bioconductor.org/packages/devel/bioc/html/KEGGgraph.html
It also seems that you may have some plot that you want to push into
PDF
format and are unsure how you might do that. Is that right? If so,
then you should only need to do something like this:
##turn on the pdf device to start output flowing to "myfile.pdf"
pdf("myfile.pdf")
##then call plot() with the appropriate arguments.
plot(Appropriate arguments here)
##then turn off that pdf device (now that you have captured the
output).
dev.off()
I hope this helps,
Marc
Hi Daniel:
This is also something in which I am interested, but have not found an
easy way yet.
If KEGG allows the network images to be downloaded in SVG format
(currently I found only GIF), then I think there is a way of manually
modifying the color of the nodes.
Within the KEGGSOAP package, there is a function called
"mark.pathway.by.objects"
Client-side interface to obtain an url for a KEGG pathway diagram with
a given set of genes marked
Description
Given a KEGG pathway id and a set of KEGG gene ids, the functions
return the URL of a KEGG
pathway diagram with the elements corresponding to the genes
marked by red or speci?ed color
I used the example code given there in:
---------------------------------------------------
url <- mark.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"))
if(interactive()){
browseURL(url)
}
url <- color.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"),
c("#ff0000", "#00ff00"), c("#ffff00"
---------------------------------------------------
And it creates an image at
http://soap.genome.jp/tmp/mark_pathway_www2_api14063/eco00260.gif with
the nodes marked.
Best wishes,
Saroj
----- Original Message -----
From: "Daniel Brewer" <daniel.brewer@icr.ac.uk>
To: "Bioconductor mailing list" <bioconductor at="" stat.math.ethz.ch="">
Sent: Thursday, April 16, 2009 6:50:44 AM GMT -05:00 US/Canada Eastern
Subject: [BioC] Visualise KEGG pathway and highlight genes
Hello,
>From a couple of interesting gene lists I have found KEGG pathways
which
contain genes from both lists. Does anyone know how to visualise
this?
I was thinking something along the lines of the KEGG pathway being
plotted and the genes from the two lists highlighted in different
colours.
I can cope with this not being done in bioconductor but would prefer
it
if the final image was exported as PDF. I have searched around
without
much luck ... it seems possible that KEGGgraph maybe able to do it but
it is not clear from vignette.
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
This e-mail message is confidential and for use by the
a...{{dropped:13}}
Hi,
I am sorry, the code from KEGGSOAP manual was incomplete in my last
email. It actually reads:
--------------
url <- mark.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"))
if(interactive()){
browseURL(url)
}
url <- color.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"),
c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
--------------
Best,
Saroj
----- Original Message -----
From: "Saroj K Mohapatra" <smohapat@vbi.vt.edu>
To: "Daniel Brewer" <daniel.brewer at="" icr.ac.uk="">
Cc: "Bioconductor mailing list" <bioconductor at="" stat.math.ethz.ch="">
Sent: Thursday, April 16, 2009 11:13:08 AM GMT -05:00 US/Canada
Eastern
Subject: Re: [BioC] Visualise KEGG pathway and highlight genes
Hi Daniel:
This is also something in which I am interested, but have not found an
easy way yet.
If KEGG allows the network images to be downloaded in SVG format
(currently I found only GIF), then I think there is a way of manually
modifying the color of the nodes.
Within the KEGGSOAP package, there is a function called
"mark.pathway.by.objects"
Client-side interface to obtain an url for a KEGG pathway diagram with
a given set of genes marked
Description
Given a KEGG pathway id and a set of KEGG gene ids, the functions
return the URL of a KEGG
pathway diagram with the elements corresponding to the genes
marked by red or speci?ed color
I used the example code given there in:
---------------------------------------------------
url <- mark.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"))
if(interactive()){
browseURL(url)
}
url <- color.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"),
c("#ff0000", "#00ff00"), c("#ffff00"
---------------------------------------------------
And it creates an image at
http://soap.genome.jp/tmp/mark_pathway_www2_api14063/eco00260.gif with
the nodes marked.
Best wishes,
Saroj
----- Original Message -----
From: "Daniel Brewer" <daniel.brewer@icr.ac.uk>
To: "Bioconductor mailing list" <bioconductor at="" stat.math.ethz.ch="">
Sent: Thursday, April 16, 2009 6:50:44 AM GMT -05:00 US/Canada Eastern
Subject: [BioC] Visualise KEGG pathway and highlight genes
Hello,
>From a couple of interesting gene lists I have found KEGG pathways
which
contain genes from both lists. Does anyone know how to visualise
this?
I was thinking something along the lines of the KEGG pathway being
plotted and the genes from the two lists highlighted in different
colours.
I can cope with this not being done in bioconductor but would prefer
it
if the final image was exported as PDF. I have searched around
without
much luck ... it seems possible that KEGGgraph maybe able to do it but
it is not clear from vignette.
Dan
--
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************
The Institute of Cancer Research: Royal Cancer Hospital, a charitable
Company Limited by Guarantee, Registered in England under Company No.
534147 with its Registered Office at 123 Old Brompton Road, London SW7
3RP.
This e-mail message is confidential and for use by the
a...{{dropped:13}}
(Thanks Marc for referring to KEGGgraph)
Hi Daniel,
In case of visualizing KEGG pathways, 'KEGGgraphApp' vignette in
the
KEGGgraph package gives two examples. In principle one could draw the
graph
object acquired from KEGG via KEGGgraph package with Rgrapvhiz
package.
A toy code snippet:
library(KEGGgraph); library(Rgraphviz)
>
somegraph <- parseKKGML2Graph(xmlFile)
pdf("filename.pdf")
>
plot(somegraph, "neato")
>
dev.off()
>
>
In the KEGGgraph package there are several files attached as
examples, you
could try to use them as a starting point. Currently the KGML files on
KEGG
database webserver are not consistent and I believe the staffs are
working
on it (see the other email in the mailing list titled 'KEGGgraph,
error'), I
will post then when the KGML files are functional again.
In case of questions please do not hestitate to ask me.
Best wishes,
David
2009/4/16 Daniel Brewer <daniel.brewer@icr.ac.uk>
> Hello,
>
> >From a couple of interesting gene lists I have found KEGG pathways
which
> contain genes from both lists. Does anyone know how to visualise
this?
> I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different
colours.
>
> I can cope with this not being done in bioconductor but would prefer
it
> if the final image was exported as PDF. I have searched around
without
> much luck ... it seems possible that KEGGgraph maybe able to do it
but
> it is not clear from vignette.
>
> Dan
>
> --
> **************************************************************
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> Email: daniel.brewer@icr.ac.uk
> **************************************************************
>
> The Institute of Cancer Research: Royal Cancer Hospital, a
charitable
> Company Limited by Guarantee, Registered in England under Company
No. 534147
> with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by
the...{{dropped:19}}
Hi Daniel,
Daniel Brewer <daniel.brewer at="" icr.ac.uk="">
writes:
>
>>From a couple of interesting gene lists I have found KEGG pathways
which
> contain genes from both lists. Does anyone know how to visualise
this?
> I was thinking something along the lines of the KEGG pathway being
> plotted and the genes from the two lists highlighted in different
colours.
>
> I can cope with this not being done in bioconductor but would prefer
it
> if the final image was exported as PDF.
if a non-bioconductor solution is ok for you, you should have a look
at
pathvisio or genmapp. These programs are able to visualize expression
data in a pathway context. Some pathways KEGG pathways can directly be
used from wikipathways, others you have to convert yourself.
http://www.pathvisio.org/Main_Pagehttp://www.genmapp.org/
Hope that helps,
Georg
Hi Daniel,
If you wish to convert the gif generated at the specific url (taking
advantage of the KEGGSOAP package) to a PDF then you can use the
awesome EBImage package (which relies on the ImageMagick suit) in this
way:
## Using the example from the KEGGSOAP manual
library(KEGGSOAP)
url <- color.pathway.by.objects("path:eco00260",
c("eco:b0002", "eco:c00263"),
c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
library(EBImage)
filename="KEGGMAP.pdf" # the extension is mandatory
im.gif <- readImage(url, TrueColor)
writeImage(im.gif, filename)
Regards,
Paolo
This solution is exactly what I am looking for in my previous post.
How to improve the resolution ?
On Fri, Apr 17, 2009 at 6:29 PM, Paolo Sonego <paolo.sonego at="" gmail.com=""> wrote:
> Hi Daniel,
> If you wish to convert the gif generated at the specific url (taking
> advantage of the KEGGSOAP package) to a PDF then you can use ?the
awesome
> EBImage package (which relies on the ImageMagick suit) in this way:
>
> ## Using the example from the KEGGSOAP manual
>
> library(KEGGSOAP)
> url <- color.pathway.by.objects("path:eco00260",
> ? ? ? ? ? ? ? c("eco:b0002", "eco:c00263"),
> ? ? ? ? ? ? ? c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
>
>
> library(EBImage)
> filename="KEGGMAP.pdf" # the extension is mandatory im.gif <-
readImage(url,
> TrueColor)
> writeImage(im.gif, filename)
>
>
>
> Regards,
> Paolo
>
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