Venn diagrams

[idonaldson]

Hi,

Does anyone have a method of generating Venn diagrams that has circles with diameters proportional to the number of items in each comparison?

I have looked around for a tool to do this, but they all seem to have their own limitations.

Thanks,
Ian

[ffinkernagel]

Funny you'd ask that right now, I started coding a python library this morning, following Chow and Ruskey "Drawing Area-Proportional Venn and Euler Diagrams". , since I also could'nt find a decent (scriptable) tool.

They summarize that for 3 sets, this can't always be done with circles.

[mgogol]

You may want to look at 3venn and vennmaster.

[ffinkernagel]

All right, I've uploaded my code (which does 2 set proportional diagrams so far, and hands off everything else to R and Vennerable (which has up to 9 sets, but no proportions)) to google code at https://code.google.com/p/pyvenn/

Feedback's always welcome.

So long,
Florian

[mgogol]

Some limitations, but here's some...

http://www.cs.kent.ac.uk/people/staff/pjr/EulerVennCircles/EulerVennApplet.html

http://theory.cs.uvic.ca/euler/DrawVenn/

http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=6116&objectType=File

http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm/

[idonaldson]

Thanks for your replies. ffinkernagels new script works well for two sets and is simple to output. Any tips for using your script for three or more sets?

[ffinkernagel]

yes, please hold on a couple of days (or code the command line interface for more than 2 sets, if all you need is non proportional sets - it talks to R/vennerable for this for now).

Here were my requirements that ruled out most of the above:
-it needs to do proportional venn sets (no vennerable)
-it needs to be scriptable (from python, vennerable and rpy2 work well for this, but basically all gui only software is out (though you can call venn master from the command line, if you're willing to script temporary file creation)
-it needs to be free (DrawVenn is, but you *may not* use it's output without written permission..., Matlab is not a dependency I want to entertain)
-it needs to be correct (that means falling back on 'near rectangles' when circles don't work out for the 3 set case)

[Thomas Doktor]

Tested out your script Florian and it works like a charm The usage description needs to be updated in the source however. Thanks for making it publicly available.

The wiki page on Venn diagrams linked to yet another website tools for generating Venn diagrams with up to 4 sets: http://bioinfogp.cnb.csic.es/tools/venny/index.html
As input it takes lists of entries (could be gene names).

[steven]

Tested out your script Florian and it works like a charm The usage description needs to be updated in the source however. Thanks for making it publicly available.

The wiki page on Venn diagrams linked to yet another website tools for generating Venn diagrams with up to 4 sets: http://bioinfogp.cnb.csic.es/tools/venny/index.html
As input it takes lists of entries (could be gene names).

This precise one (Venny) has been recently used in this analysis:
"The primary transcriptome of the major human pathogen Helicobacter pylori"
Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jérémy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler & Jörg Vogel
Nature advance online publication 17 February 2010
doi:10.1038/nature08756

[mattanswers]

Here is another place where you can make Venn diagrams:

http://www.cmbi.ru.nl/cdd/biovenn/

[apratap]

Here is something from Google Visualization API.

http://code.google.com/apis/chart/docs/gallery/venn_charts.html

-A

[tebuffer]

any number of sets - proportional venn diagram

i have been using the following offline tool (vennmaster) for quite some time.

Excellent tool to proportionately draw several sets.

http://www.informatik.uni-ulm.de/ni/staff/HKestler/vennm/doc.html

TEB

[TRA]

I am using http://bioinfogp.cnb.csic.es/tools/venny/ to sort my DEG lists that resulted from RNA-Seq analysis, but some of the genes get ignored by the program.

Is any one know the reason for that?

Any help would be appreciated!