[R] Venn diagram

2007-05-31 Thread Nina Hubner
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

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Re: [R] Venn diagram

2007-05-31 Thread Adaikalavan Ramasamy
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.
 
 


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Re: [R] Venn diagram

2007-05-31 Thread Earl F. Glynn
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.


__
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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

2007-05-31 Thread Gabor Grothendieck
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.


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R-help@stat.math.ethz.ch mailing list
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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

2007-05-31 Thread Paul Artes

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.
 
 

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View this message in context: 
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Re: [R] venn diagram with more than three vectors

2006-09-26 Thread Gavin Simpson
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
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R-help@stat.math.ethz.ch mailing list
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Re: [R] venn diagram with more than three vectors

2006-09-26 Thread Oosting, J. \(PATH\)
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.


[R] venn diagram with more than three vectors

2006-09-26 Thread Pan Zheng
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


-


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and provide commented, minimal, self-contained, reproducible code.