Plot distribution of functional effects stratified by times observed in natural GPC sequences

[Caleb-Carr]

Make plots of the distribution of effects of:

• all amino-acid mutations
• amino acid mutations observed at least once in a natural GPC
• amino acids mutations observed at least N times in a natural GPC, where you make some reasonable choice of N > 1.

This is related to the following comment:

4. According to Figure 2C, most (perhaps more than 90%) of the single mutations on GPC are deleterious to viral entry. However, the GPC of different Lassa lineages seems to tolerate amino acid differences as high as ~10% (Figure 1C). The authors should provide possible explanations. Meanwhile, different Lassa lineages already have a sizeable antigenic diversity, so the application of the DMS map developed based on the Josiah strain to other lineages might be limited.

[Caleb-Carr]

@jbloom This notebook plots the distributions of functional effects of mutations stratified by times observed in natural sequences.

[jbloom]

Looks good, although you might make the top row a bit more lenient, like say >10 or > 20.

Also, the overplotting problem is pretty severe especially for the bottom category, so explore if this would look better as a boxplot.

[Caleb-Carr]

@jbloom Updated notebook to a more lenient top cutoff (>=10) and changed distributions to boxplots.

[jbloom]

Looks good.