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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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weblogo plot image artifacts. #64

Closed adalisan closed 2 years ago

adalisan commented 2 years ago

The pdf plots for differential selections that are generated sometime have weird lines instead of letters. I thought these are just squashed letters, but they sometimes are drawn across multiple sites. Despite increasing the letterheight these lines are persisting. Is this an artifact of matplotlib and pdf creation>

jbloom commented 2 years ago

Hmm, without a more detailed example I can't really answer this.

adalisan commented 2 years ago

nsp12_0 (2)

So I took a cropped screenshot of the output of the pdf. this is one of the many lines that have artifacts like this. They look like very squashed versions of some letters. But when they do appear, they are spread across multiple positions which does not make sense to me.

jbloom commented 2 years ago

That's strange. Not sure what is causing that. Honestly, I'd suggest switching to https://jbloomlab.github.io/dmslogo/ or https://logomaker.readthedocs.io/en/latest/ instead as I'm not really maintaining the logo plots for dms_tools2 anymore beyond making sure it still works on our particular setup.

adalisan commented 2 years ago

@jbloom Is there a simple example of how you would generate them in dmslogo? would you just need the csv file output of the differential statistics?

jbloom commented 2 years ago

The dmslogo documentation has some examples: https://jbloomlab.github.io/dmslogo/

Also, here is some example code from one of our projects: https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_LY-CoV555/blob/main/escape_profiles.ipynb