weblogo plot image artifacts.
adalisan opened this issue · 5 comments
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>
Hmm, without a more detailed example I can't really answer this.
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.
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.
@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?
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