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jbloomlab / polyclonal

Model mutational escape from polyclonal antibodies.
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order amino-acid alphabets differently? #109

Closed jbloom closed 1 year ago

jbloom commented 1 year ago

@Bernadetadad, I'm almost done with the milestones for what you need for the pipeline to analyze your DMS data (see here).

However, I wanted to add one more potential issue: Do we want to order the amino-acids in the rows of the heatmaps different? Right now they are alphabetical. But for instance in prior deep mutational scanning (e.g., see Fig 1 of Tyler and Allie's latest paper) we ordered them by physicochemical properties.

Should I make that the default for us too? If so, should I just use same ordering from above paper, or any preferences?

Bernadetadad commented 1 year ago

Yes, I think if amino acids are ordered by physicochemical properties that would be better than alphabetical. I think the same order as from Tyler/Allie papers works well and if we/someone else ever want to just visually compare these datasets that would be quite convenient.