Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-12T19:40:52.653Z
Answers.Text: The Python upsetplot module works pretty well!
Answers.UserDisplayName: Wouter De Coster
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-11T23:38:06.313Z
Answers.LastActivityDate: 2020-08-12T23:21:35.157Z
Answers.LastEditDate: 2020-08-12T23:21:35.157Z
Answers.UserDisplayName: Alex Reynolds
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-12T14:28:24.050Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Tags: <python><ngs><phylogenetics><visualization><pcr>
Title: Need a alternative or more complex version of venn diagram in python for matching dna sequences
ThreadText: # 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.  
  
  ---
  
  ## 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!  
  
  ---
  
  