<p>To get around limitations in using Venn diagrams for set overlaps, when there are more than three sets, <a href="https://www.biostars.org/p/77362/#77377" rel="nofollow noreferrer">back around 2013 or so</a> I created something I called an <a href="https://gist.github.com/jguenther/a13310c0403ac2c3663b" rel="nofollow noreferrer">Eulergrid</a> plot (example at the bottom of the page), which an <a href="https://cran.r-project.org/web/packages/UpSetR/vignettes/basic.usage.html" rel="nofollow noreferrer">UpsetR</a> plot appears to recapitulate, today.</p>
<p>The Eulergrid code I wrote was in a mix of Perl and R; the UpsetR plot code uses R. There appears to be a <a href="https://pypi.org/project/UpSetPlot/" rel="nofollow noreferrer">Python port</a> of UpsetR that might work, as well.</p>

CC BY-SA 4.0
2020-08-12T19:40:52.653Z
The Python upsetplot module works pretty well!
Wouter De Coster
CC BY-SA 4.0
2020-08-11T23:38:06.313Z
2020-08-12T23:21:35.157Z
2020-08-12T23:21:35.157Z
Alex Reynolds
<p>I am in google colab and I have combined and set up a data frame list of sequences that goes like this</p>
<p>Location ID Sequence</p>
<p>1.1     ........ A ........ AAGAGATA</p>
<p>1.2     ........ A...........   CGGATGAT</p>
<p>1.3     ........ B................   ACGTGATC</p>
<p>1.1     ........ B ........ AAGAGATA</p>
<p>1.2     ........ B...........   CGGATGAT</p>
<p>1.3     ........ C................   ACGTGATC</p>
<p>So I need to make a alternative to Venn diagram because there are about 20+ ID types within a couple hundred rows of list just like this. And some of the sequences repeat or are unique to its id so I need something to be like</p>
<p>CGGATGAT Shows up 4 times in B,C,A, and D
ACGTGATC shows up 1 time in B
AGTGTCTC shows up 5 times in E,A,B,C, and D.</p>
<p>And then have some kind of graphical visualation to show all of these common sequences and where they are located and which are unique. Using python. This might be asking for too much but I'm not sure. I would use something like vennr to make a bigger complex version of <a href="https://raw.githubusercontent.com/montilab/vennr/master/README_files/figure-gfm/unnamed-chunk-7-1.png" rel="nofollow noreferrer">this</a> but I don't really know R.</p>

CC BY-SA 4.0
2020-08-12T14:28:24.050Z
Something like this, perhaps? https://64.media.tumblr.com/tumblr_m723nmp5OM1qbh26io1_1280.jpg (http://www.promusa.org/blogpost174-The-best-genomics-Venn-diagram-ever-deconstructed). Bear in mind that there is likely no way to visualize this that will be as effective as a table of numbers.
terdon
<python><ngs><phylogenetics><visualization><pcr>
Need a alternative or more complex version of venn diagram in python for matching dna sequences
# Need a alternative or more complex version of venn diagram in python for matching dna sequences

(Asked by: username_0 on 2020-08-11)

I am in google colab and I have combined and set up a data frame list of sequences that goes like this

Location ID Sequence

1.1 ........ A ........ AAGAGATA

1.2 ........ A........... CGGATGAT

1.3 ........ B................ ACGTGATC

1.1 ........ B ........ AAGAGATA

1.2 ........ B........... CGGATGAT

1.3 ........ C................ ACGTGATC

So I need to make a alternative to Venn diagram because there are about 20+ ID types within a couple hundred rows of list just like this. And some of the sequences repeat or are unique to its id so I need something to be like

CGGATGAT Shows up 4 times in B,C,A, and D
ACGTGATC shows up 1 time in B
AGTGTCTC shows up 5 times in E,A,B,C, and D.

And then have some kind of graphical visualation to show all of these common sequences and where they are located and which are unique. Using python. This might be asking for too much but I'm not sure. I would use something like vennr to make a bigger complex version of [this](https://raw.githubusercontent.com/montilab/vennr/master/README_files/figure-gfm/unnamed-chunk-7-1.png) but I don't really know R.

**Tags:** python, ngs, phylogenetics, visualization, pcr
> **Comments:**
> **username_1**: Something like this, perhaps? https://64.media.tumblr.com/tumblr_m723nmp5OM1qbh26io1_1280.jpg (http://www.promusa.org/blogpost174-The-best-genomics-Venn-diagram-ever-deconstructed). Bear in mind that there is likely no way to visualize this that will be as effective as a table of numbers.  

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## 1 answers

### Answer by username_2 on 2020-08-11. Score: 5

To get around limitations in using Venn diagrams for set overlaps, when there are more than three sets, [back around 2013 or so](https://www.biostars.org/p/77362/#77377) I created something I called an [Eulergrid](https://gist.github.com/jguenther/a13310c0403ac2c3663b) plot (example at the bottom of the page), which an [UpsetR](https://cran.r-project.org/web/packages/UpSetR/vignettes/basic.usage.html) plot appears to recapitulate, today.

The Eulergrid code I wrote was in a mix of Perl and R; the UpsetR plot code uses R. There appears to be a [Python port](https://pypi.org/project/UpSetPlot/) of UpsetR that might work, as well.

> **Comments:**
> **username_3**: The Python upsetplot module works pretty well!  

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