R help - May 2007 - 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

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 at 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.
> 
> 
>

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" <nina.hubner at web.de> wrote in message 
news:loom.20070531T115942-677 at post.gmane.org...
> 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 at 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.
>

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 at 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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