Question: How to draw venn diagram for two CNV lists?
0
6.0 years ago by
lyz10302012360
China
lyz10302012360 wrote:

I want to draw the venn diagram for two CNV lists. I use a 1-bp reciprocal overlap criterion to declare two CNVs are same.

My question is if one element in list 1 overlaps with multi elements in list 2, how can I interpret intersect?

i.e.

Size of list1: 100

Size of list2: 200

10 CNVs in list1 overlaps with 20 cnvs in list2

Here my question is how to determine the intersect, is it 10 ,20 or both? How can I draw the venn diagram?

tool venn • 3.7k views
modified 2.3 years ago by lieven.sterck9.0k • written 6.0 years ago by lyz10302012360

10 CNVs in list1 overlaps with 20 cnvs in list2 It means there are duplicates in list. While drawing Venn we consider only unique values. Hope I answered your question

1
6.0 years ago by
Jie Ping30
China
Jie Ping30 wrote:

http://bioinfogp.cnb.csic.es/tools/venny/index.html

Venny was down today... In any event, I would highly recommend I would highly recommend VENDIS:

http://kislingerlab.uhnres.utoronto.ca/projects/VennDIS_v1.0.zip

It just came out and it's really quite good!

1
6.0 years ago by
Rodons10
European Union
Rodons10 wrote:

You can also use biovenn (http://www.cmbi.ru.nl/cdd/biovenn/index.php), which will also recognize your entries and will link them.

1
6.0 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

I am not a CNV expert (or genomics, for that matter), but I think it boils down to the question you are asking. Are you counting the number of overlapping CNVs when comparing sample 1 to sample 2, or sample 2 to sample 1? I think both would be fine, as long as you make sure to write which comparison you are making.

0
6.0 years ago by
Nandini880
Nandini880 wrote:

You can easily do it in R but if you want to opt for a software, I find this tool very useful http://omics.pnl.gov/software/venn-diagram-plotter

0
6.0 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

Here is a good StackOverflow post on creating Venn diagrams in R:

http://stackoverflow.com/questions/1428946/venn-diagrams-with-r

0
6.0 years ago by
lyz10302012360
China
lyz10302012360 wrote:

Here my question is how to determine the intersect, is it 10 or 20?

0
2.3 years ago by
shalin30
shalin30 wrote:

Its probably best to use use a Venn Diagram Maker like Creately. Its an online diagramming & collaboration software to draw Venn diagrams. There are all the objects and shapes necessary to create Venn and Euler diagrams with 100s of templates and examples to be used freely.

0
2.3 years ago by
lieven.sterck9.0k
VIB, Ghent, Belgium
lieven.sterck9.0k wrote:

and here is another alternative (draws up to 6 intersections): Draw Venn