PspA figure implementation

[falquaddoomi]

Description

This PR contains a very work-in-progress implementation of figure 4 from the PspA paper, https://journals.asm.org/doi/epub/10.1128/msystems.00847-23. The PR
is intended as a starting point, so you don't have to go and find the original code from the papers, but it definitely needs a lot of work! See issue #90 for more details.

Closes #90.

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

• I have read and followed the CONTRIBUTING.md guidelines.
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• I have performed a self-review of these additions (including spelling, grammar, and related).
• I have added comments to my code to help provide understanding.
• I have added a test which covers the code changes found within this PR.
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[jananiravi]

I've moved things around a bit to at least clean up towards a working function. It's clearly not quite there yet. I hope this helps as a start.
I need a little help, @the-mayer @epbrenner -- thanks!

[falquaddoomi]

Hey @jananiravi, thanks for the review. Would it be alright if I committed your suggestions? They all seem reasonable to me. (Well, since molevol_scripts is directly sourced by the Shiny app, not imported as a package, I'll likely keep the library() calls and other source() statements that refer to the rest of the code, just so things work, but I'll keep removing them in mind for when we go back to making all these figure-generating functions package methods.)

Also, I was planning to create a new PR in https://github.com/JRaviLab/molevol_scripts with this PR's contents. I had originally created PRs here for each figure so our contributors could work on it, but since no one took it on and it's needed for the rebuttal I was thinking it'd be faster to get it merged into molevol_scripts first. When we're ready, I can port it back over to the package.

If that's all OK with you I'll start working on that, and I'll do the same for DciA and InlP.

[jananiravi]

Sounds good, Faisal. If you have any additional questions, please feel free to tag @epbrenner and me, and we will get back to you ASAP. Thanks!