@Bernadetadad, I merged a pull request that made some logo plots. I am imagining these could go in Figure 3.
The notebook that makes the logo plots is here, and it shows them albeit at limited resolution:
However, SVGs are also saved to a subdirectory, and those are probably what to use for figures.
Below is sort of what I was imagining. If you think these should be revised / updated, just re-open this issue with the requested changes.
Figure 3C could be logo plots showing the key sites of escape (after averaging across sera) colored by ACE2 affinity.
There is an ACE2 affinity scale bar here or here. Panel C could contain that along with this plot. The key point would therefore be to provide more zoomed in information on key sites, and also at least partly explain why for instance we see evolution at some sites but not others (eg, Y473). I think this could be a nice detailed way to call out key sites of escape and sort of show how some have a ACE2 binding tradeoff.
The text can also then say how there is a lot of heterogeneity across sera at these key sites and refer to both the current Figure 3A,B and a supplementary figure with per-sera logos. Per-sera logos are here for all mutations and here for single-nucleotide. You would probably want to re-make in a two-column 5 row figure? I would lean towards showing the one with all mutations rather than single-nucleotide, as the point of this plot would be the serum heterogeneity.
Then we want to show something to go alongside the neuts. I made the following image here. I am imagining you could potentially put neut panels side-by-side (to right of each row) of these? I feel like what we would want to say is "We picked mutations to validate. Some of these mutations had similar sites across all sera either escaping (eg, R357H) or sensitizing (eg, N405K). But others had very different effects across sera (eg, Y473S). All these mutations validated."
@Bernadetadad, I merged a pull request that made some logo plots. I am imagining these could go in Figure 3.
The notebook that makes the logo plots is here, and it shows them albeit at limited resolution:
However, SVGs are also saved to a subdirectory, and those are probably what to use for figures.
Below is sort of what I was imagining. If you think these should be revised / updated, just re-open this issue with the requested changes.
Figure 3C could be logo plots showing the key sites of escape (after averaging across sera) colored by ACE2 affinity.
There is an ACE2 affinity scale bar here or here. Panel C could contain that along with this plot. The key point would therefore be to provide more zoomed in information on key sites, and also at least partly explain why for instance we see evolution at some sites but not others (eg, Y473). I think this could be a nice detailed way to call out key sites of escape and sort of show how some have a ACE2 binding tradeoff.
The text can also then say how there is a lot of heterogeneity across sera at these key sites and refer to both the current Figure 3A,B and a supplementary figure with per-sera logos. Per-sera logos are here for all mutations and here for single-nucleotide. You would probably want to re-make in a two-column 5 row figure? I would lean towards showing the one with all mutations rather than single-nucleotide, as the point of this plot would be the serum heterogeneity.
Then we want to show something to go alongside the neuts. I made the following image here. I am imagining you could potentially put neut panels side-by-side (to right of each row) of these? I feel like what we would want to say is "We picked mutations to validate. Some of these mutations had similar sites across all sera either escaping (eg, R357H) or sensitizing (eg, N405K). But others had very different effects across sera (eg, Y473S). All these mutations validated."
Anyway, let me know what you think!