InlP figures implementation

[falquaddoomi]

Description

This PR contains a very work-in-progress implementation of figures 2 and 3 from the InlP paper, https://www.microbiologyresearch.org/docserver/fulltext/mgen/8/7/mgen000828.pdf. 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 #88 for more details.

Closes #88.

What kind of change(s) are included?

• [x] 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.

• [x] I have read and followed the CONTRIBUTING.md guidelines.
• [x] I have searched for existing content to ensure this is not a duplicate.
• [ ] 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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[valentina-buoro]

Hi @epbrenner @jananiravi .

I tried running some files in the job results folder with the figure-generating code, and I'm getting an error Error in plan(strategy = plan, .skip = T) : could not find function "plan" . Searching the code for the plan function gave no results. Pls could you give me a pointer to what may be going on. The function I ran was inlp_fig2 .

[jananiravi]

@falquaddoomi @epbrenner could you look into this?

[falquaddoomi]

So, I'm not an R developer, so take this all with a grain of salt. Anyway...

@valentina-buoro, plan is from the future library; it basically tells R how to resolve "futures", functions that can be executed asynchronously (i.e., not in the main thread). Since it's in the future library, adding library(future) somewhere near the top of the file should resolve it.

I'm not sure why you're getting that message, though. The plan() invocation is almost certainly coming from another library, which is why you're not seeing it in the code, but I don't know enough about R to say whether the author of that library is correctly loading future or if that's the user's responsibility.

[jananiravi]

If we know for sure that we're invoking future::plan() best to call it explicitly to avoid any confusion. @the-mayer are we using future enough to warrant adding it as a dependency (to function imports)? Then even the library call upfront in this script might not be needed.

Thanks for addressing this, @falquaddoomi

[valentina-buoro]

Thank you @falquaddoomi @jananiravi

[the-mayer]

Another way to make sure all dependencies are loaded when working on a package is to run devtools::load_all(). This will attempt to load all MolEvolvR exported functions, as well as any declared imports. future::plan() is declared in the package NAMESPACE and thus would be loaded by a call to devtools::load_all()

[valentina-buoro]

Got it @the-mayer . Thank you