Bernadetadad
commented
1 year ago I'm actually showing mean escape plot in fig3 and in mean plot is major sites seem more consistent if those filters are changed. But I agree we should probably explicitly call this out, it's important to emphasize that we don't know what those filters should. I think Y200C might be the worst affinity mutation (-0.67) that I can name of the top of my head having come up in successful major lineage but there are probably others.
Looking at the summary plot, the impression of what is the greatest escape sites is substantially influenced by the ACE2 and functional effects filters. For instance, if those are -2 then the peak escape site is 473. When they are at -1.5 several sites have much more escape than 473.
Anyway, just bringing this up to spur more thought about how we set these filters. If we are arguing "we measure three phenotypes and see how they relate to evolution," then do we want to avoid setting the filters on the affinity / functional effects so stringently that it affects the visual display of the escape phenotype? Or maybe we want to keep the filters at -1.5 but then I think we should explicitly call this out, such as by showing escape profile in paper for several different filter values.
@Bernadetadad, thoughts?