start making nice VitePress documentation

[jbloom]

@Bernadetadad, I'm going to start making some nice VitePress documentation for the pipeline with key plots. Let me know if there is anything specific you think this should include.

One thing I was going to make was additional summary plots that show the most relevant phenotypes, and then add those with nice labels.

[Bernadetadad]

I find the way summary plots are currently displayed to be very "clunky", mostly because we have so many phenotypes it's almost impossible to look at them all in the summary page right now (certainly not on a standard laptop). And (maybe it's just me) but when you hover over heatmaps in summary page there's always an annoying delay probably because so much data is being displayed. I don't know how to solve this, I see advantage in displaying everything, but I at least would wonder if a nice landing page that shows all four phenotypes and then summary pages for individual phenotypes as opposed to everything might be better (and perhaps just showing values from other phenotypes when hovering over specific sites could be an option).

[jbloom]

Agreed, I will work on this in some way.

Part (most) of what makes it so big is showing all the different serum escapes. I will look into a stripped down summary plot that does that more effectively as well.

[jbloom]

@Bernadetadad, I just merged #72, which makes two summary plots. Major changes:

• one summary plot just shows the average of each species
• another shows all antibody-escape. This one remains large
• only SA26 improvement is shown as phenotype
• I tried to standardize floors, filters, etc.

This broke your all_phenotypes rule, but I can fix that tomorrow.

For now, can you look over plots and:

• make comments about things that could be improved in appearance, what is shown, or filters
• help me check filters are consistent internally in pipeline, and defaults for plot visualizations (mean versus sum, floors, filters, etc) match what you are using as static plots for figures.

Just either comment on this issue or raise new issues as appropriate (depending on if it is discrete thing to fix = new issue, or general discussion = this issue).

I will also go over this to look more myself tomorrow.

[Bernadetadad]

• Maybe it would be possible to have two colors for 'individual species escape' in overlayed summary? It's really hard to see even two lines when they are so similar and both grey.
• Filters look consistent

[jbloom]

@Bernadetadad, for your particular request re the coloring individual species escape, I am running into trouble getting this working and I think there will be a lot of overlap regardless. For this purpose, can we just use the faceted chart, which I think shows the two species clearly.