[FEAT] Fix, Implement InlP Figure

[falquaddoomi]

We need to add figures 2 and 3 from the InlP paper, https://www.microbiologyresearch.org/docserver/fulltext/mgen/8/7/mgen000828.pdf. We have some code, written when the paper was published, that was used to generate those figures, but it's likely out of date and wasn't written to use MolEvolvR's job outputs. The figure will need to be integrated into the MolEvolvR web app, both for displaying on the site and including in the downloadable report.

Any progress on the following tasks would be appreciated:

• getting the figure to render with its original inputs
• adapting the code to use MolEvolvR's job output

I've included a sample MolEvolvR job output, 5uNQ9l, to demonstrate what files are typically included in a MolEvolvR job.

5uNQ9l_full.tar.gz

See PR #91 for the current code. If you self-assign this issue also assign yourself to that PR. Once your PR is ready, you can convert it from a draft to a regular PR and request review. If you prefer to not use that PR as a starting point, you're also free to create your own.

[valentina-buoro]

Hi @falquaddoomi I'd like to work on this

[jananiravi]

Let us know if anything is unclear, @valentina-buoro.

[valentina-buoro]

Hi @falquaddoomi , can I use data from this inlp repo https://github.com/JRaviLab/inlp_listeria to test the visualization for this task?

[falquaddoomi]

Hi @valentina-buoro, I believe so, but @jananiravi would be able to give you a more sure answer.

[valentina-buoro]

Okay. The reason why I asked is because I don't seem to have access to the source code for the figurehttps://github.com/JRaviLab/molevol_data/blob/main/scripts/inlp/inlp_dual_plot.R and the table https://github.com/JRaviLab/molevol_data/blob/main/scripts/inlp/inlp_make_table.R @falquaddoomi @jananiravi

[falquaddoomi]

@valentina-buoro I've just invited you to have read access to molevol_data, FYI, just in case you need it.

[valentina-buoro]

Thank you @falquaddoomi

[valentina-buoro]

@falquaddoomi , I'm trying to run the current code in #91 so I can see how it currently outputs the figure and table, but the input files used are not included in the sample MolEvolvR job output, 5uNQ9l attached to this issue. How can I resolve this please?

[falquaddoomi]

Hey @valentina-buoro, that's kind of the meat of the issue: figuring out which, if any, of the files in the job results folder is similar to what the figure-generating code requires, and if not where to find the files it needs.

Just for some background, the figure-generating code from #91 has never actually been used in MolEvolvR; it was lifted from the original repo for the paper with the intent of integrating it into MolEvolvR, but it hadn't been integrated yet. You might consider touching base with @jananiravi or @epbrenner who likely have more insight into that code; I'm not familiar with it myself.

[valentina-buoro]

Thanks for the clarification @falquaddoomi

[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]

plan might be from the futures package. Also, I second Faisal's point. There are two primary file formats -- the tsv from the homolog tab and the iprscan file used by ipr2viz in the domain architecture tab. @epbrenner is this latter file now downloadable from molevolvr along with the new report generator by @the-mayer

[valentina-buoro]

Okay. Thank you @jananiravi .