Re: [R] Venn diagram
I'm really glad to see this topic come up. Area-proportional Venn diagrams
are a phantastic way to visualize agreement. For the 2-rater scenario this
is straightforward; here are two examples from my own work that were done in
R. (I'm far too embarrassed to enclose the code).
http://myweb.dal.ca/partes/venn_example.jpg
For 3 (or more!) variables, it becomes tricky, but Chow and Ruskey have
solved this recently (see link below).
http://www.cs.uvic.ca/~ruskey/Publications/VennArea/VennArea.html
I think there is even a Java applet for demonstration purposes.
It would be phantastic to have a good R-implementation of this...
Unfortunately my own skills are several log units below what's required. I
have written to Chow and Ruskey before but unfortunately not heard anything.
Anyone up for the job??
Best wishes
Paul
Nina Hubner wrote:
>
> Hello,
>
>
>
> I am a total beginner with “R” and found a package “venn” to
> create a venn diagram.
>
> The problem is, I cannot create the vectors required for the diagram.
>
> The manual say:
> "R> venn(accession, libname, main = "All samples")
> where accession was a vector containing the codes identifying
> the RNA sequences, and libname was a vector containing the codes
> identifying the tissue sample (library)."
>
>
> The structure of my data is as follows:
>
>
>
> R> structure(list(cyto = c("A", “B”, “C”, “D”), nuc = c(“A”, “B”, “E”,
> “”),
> chrom = c(“B”, “F”, “”, “”)),.Names = c("cyto", "Nuc", "chrom"))
>
>
> accession should be "A", "B", and libname schould be "cyto",
> "nuc" and "chrom" as I understand it...
>
>
> Could you help me?
>
>
>
> Sorry, that might be a very simple question, but I am a total beginner
> as said before! The question has already been asked, but unfortunately
> there was no answer...
>
>
>
> Thank you a lot,
>
> Nina Hubner
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
--
View this message in context:
http://www.nabble.com/Venn-diagram-tf3846402.html#a10897668
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Venn diagram
There is a venn package at these links:
http://fisher.stats.uwo.ca/faculty/murdoch/repos/html/vennv1.5.html
http://www.jstatsoft.org/v11/c01/
On 5/31/07, Earl F. Glynn <[EMAIL PROTECTED]> wrote:
> I'm not sure where you're getting the "venn" package. I don't find "venn" in
> either of these places:
>
> - http://cran.r-project.org/src/contrib/PACKAGES.html
> - http://www.bioconductor.org/packages/release/Software.html
>
> In case this helps, here are some notes about creating Venn Diagrams using
> the limma package:
> http://research.stowers-institute.org/efg/R/Math/VennDiagram.htm
>
> efg
> Stowers Institute for Medical Research
>
>
> "Nina Hubner" <[EMAIL PROTECTED]> wrote in message
> news:[EMAIL PROTECTED]
> > Hello,
> >
> >
> >
> > I am a total beginner with "R" and found a package "venn" to
> > create a venn diagram.
> >
> > The problem is, I cannot create the vectors required for the diagram.
> >
> > The manual say:
> > "R> venn(accession, libname, main = "All samples")
> > where accession was a vector containing the codes identifying
> > the RNA sequences, and libname was a vector containing the codes
> > identifying the tissue sample (library)."
> >
> >
> > The structure of my data is as follows:
> >
> >
> >
> > R> structure(list(cyto = c("A", "B", "C", "D"), nuc = c("A", "B", "E",
> > ""),
> > chrom = c("B", "F", "", "")),.Names = c("cyto", "Nuc", "chrom"))
> >
> >
> > accession should be "A", "B", and libname schould be "cyto",
> > "nuc" and "chrom" as I understand it...
> >
> >
> > Could you help me?
> >
> >
> >
> > Sorry, that might be a very simple question, but I am a total beginner
> > as said before! The question has already been asked, but unfortunately
> > there was no answer...
> >
> >
> >
> > Thank you a lot,
> >
> > Nina Hubner
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Venn diagram
I'm not sure where you're getting the "venn" package. I don't find "venn" in
either of these places:
- http://cran.r-project.org/src/contrib/PACKAGES.html
- http://www.bioconductor.org/packages/release/Software.html
In case this helps, here are some notes about creating Venn Diagrams using
the limma package:
http://research.stowers-institute.org/efg/R/Math/VennDiagram.htm
efg
Stowers Institute for Medical Research
"Nina Hubner" <[EMAIL PROTECTED]> wrote in message
news:[EMAIL PROTECTED]
> Hello,
>
>
>
> I am a total beginner with "R" and found a package "venn" to
> create a venn diagram.
>
> The problem is, I cannot create the vectors required for the diagram.
>
> The manual say:
> "R> venn(accession, libname, main = "All samples")
> where accession was a vector containing the codes identifying
> the RNA sequences, and libname was a vector containing the codes
> identifying the tissue sample (library)."
>
>
> The structure of my data is as follows:
>
>
>
> R> structure(list(cyto = c("A", "B", "C", "D"), nuc = c("A", "B", "E",
> ""),
> chrom = c("B", "F", "", "")),.Names = c("cyto", "Nuc", "chrom"))
>
>
> accession should be "A", "B", and libname schould be "cyto",
> "nuc" and "chrom" as I understand it...
>
>
> Could you help me?
>
>
>
> Sorry, that might be a very simple question, but I am a total beginner
> as said before! The question has already been asked, but unfortunately
> there was no answer...
>
>
>
> Thank you a lot,
>
> Nina Hubner
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Venn diagram
I cannot find the venn package (searched the author's page and googled)
despite some posts referring to it, so I cannot help you. But I can
suggest you check out the varpart in vegan package, vennDiagram in limma
package or http://finzi.psych.upenn.edu/R/Rhelp02a/archive/14637.html
Regards, Adai
Nina Hubner wrote:
> Hello,
>
>
>
> I am a total beginner with “R” and found a package “venn” to
> create a venn diagram.
>
> The problem is, I cannot create the vectors required for the diagram.
>
> The manual say:
> "R> venn(accession, libname, main = "All samples")
> where accession was a vector containing the codes identifying
> the RNA sequences, and libname was a vector containing the codes
> identifying the tissue sample (library)."
>
>
> The structure of my data is as follows:
>
>
>
> R> structure(list(cyto = c("A", “B”, “C”, “D”), nuc = c(“A”, “B”, “E”, “”),
> chrom = c(“B”, “F”, “”, “”)),.Names = c("cyto", "Nuc", "chrom"))
>
>
> accession should be "A", "B", and libname schould be "cyto",
> "nuc" and "chrom" as I understand it...
>
>
> Could you help me?
>
>
>
> Sorry, that might be a very simple question, but I am a total beginner
> as said before! The question has already been asked, but unfortunately
> there was no answer...
>
>
>
> Thank you a lot,
>
> Nina Hubner
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Venn diagram
Hello,
I am a total beginner with “R” and found a package “venn” to
create a venn diagram.
The problem is, I cannot create the vectors required for the diagram.
The manual say:
"R> venn(accession, libname, main = "All samples")
where accession was a vector containing the codes identifying
the RNA sequences, and libname was a vector containing the codes
identifying the tissue sample (library)."
The structure of my data is as follows:
R> structure(list(cyto = c("A", “B”, “C”, “D”), nuc = c(“A”, “B”, “E”, “”),
chrom = c(“B”, “F”, “”, “”)),.Names = c("cyto", "Nuc", "chrom"))
accession should be "A", "B", and libname schould be "cyto",
"nuc" and "chrom" as I understand it...
Could you help me?
Sorry, that might be a very simple question, but I am a total beginner
as said before! The question has already been asked, but unfortunately
there was no answer...
Thank you a lot,
Nina Hubner
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] venn diagram with more than three vectors
I am not aware of existing functions to draw venn diagrams with more than 3 sets, but you could have a look at http://en.wikipedia.org/wiki/Venn_diagram to see how these can be constructed. Jan Oosting -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Pan Zheng Sent: dinsdag 26 september 2006 2:09 To: r-help@stat.math.ethz.ch Subject: [R] venn diagram with more than three vectors Hi, I am using venn diagram function in AMDA to plot the venn diagram. But it seems in this function, it can only plot 3 or less vectors. Is there a way to plot the venn diagram with more than 3 vectors? Please help. Thanks. Z __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] venn diagram with more than three vectors
On Tue, 2006-09-26 at 10:02 +0200, Oosting, J. (PATH) wrote: > I am not aware of existing functions to draw venn diagrams with more > than 3 sets, but you could have a look at > http://en.wikipedia.org/wiki/Venn_diagram to see how these can be > constructed. > > Jan Oosting Package vegan has a function (varpart) and plot method that will draw venn diagrams with up to 4 sets. It works on results from redundancy analyses, but you could probably adapt it to your needs. HTH G > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Pan Zheng > Sent: dinsdag 26 september 2006 2:09 > To: r-help@stat.math.ethz.ch > Subject: [R] venn diagram with more than three vectors > > Hi, > > I am using venn diagram function in AMDA to plot the venn diagram. But > it seems in this function, it can only plot 3 or less vectors. Is there > a way to plot the venn diagram with more than 3 vectors? > > Please help. > > Thanks. > > Z > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% *Note new Address and Fax and Telephone numbers from 10th April 2006* %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC [f] +44 (0)20 7679 0565 UCL Department of Geography Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street London, UK[w] http://www.ucl.ac.uk/~ucfagls/cv/ WC1E 6BT [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] venn diagram with more than three vectors
Hi, I am using venn diagram function in AMDA to plot the venn diagram. But it seems in this function, it can only plot 3 or less vectors. Is there a way to plot the venn diagram with more than 3 vectors? Please help. Thanks. Z - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
