Define R API functions in separate script

[bmeluch]

This PR pulls the R API function definitions out of notebooks and defines them all in a single R script, so we aren't accidentally defining the same function with different tweaks in different notebooks.

It modifies two existing notebooks and adds a script utility_functions.R

(Eventually this may become an R package, but R scripts seem to play nicer than R packages when embedded in a repo.)

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NOM notebook in nbviewer and colab:

https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/NOM_visualizations/R/NOM_R_notebook.ipynb

https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/NOM_visualizations/R/NOM_R_notebook.ipynb

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Taxonomy notebook in colab:

https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb

https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb

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[kheal]

The text for part 2 is rendering oddly - see above.

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[kheal]

Same comment at re: Step 2

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[kheal]

Oops, we reference "omics processing" here - please change to data generation

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[kheal]

Text rendering oddly in step 7

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[kheal]

Text rendering oddly in previous chunk

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[kheal]

@bmeluch - the sourcing for the functions doesn't work in google colab.

Here's a link to the NOM notebook in this branch in google colab - it'd be good to have this in the PR description because this is something we should be testing during each new notebook. When I try to run the first cell, it errors out with the new sourcing. I'm pretty sure @samobermiller had figured out a workaround for the python functions to make this work, hopefully the same will work for R?

NOM notebook in colab:
https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/NOM_visualizations/R/NOM_R_notebook.ipynb

Taxonomy notebook in colab:
https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/90-modularize-r-api-wrapper-functions/taxonomic_dist_by_soil_layer/R/taxonomic_dist_soil_layer_R.ipynb

[bmeluch]

The R script sourcing in Colab should work now (thank you for the links @kheal ! )
Some of the weird formatting in the taxonomy notebook is fixed, but not all - I really don't know what's going on there since it only looks weird in ReviewNB, but I'll keep trying.
This PR is temporarily blocked on re-rendering the taxonomy notebook once NERSC is back up next week.

[kheal]

@bmeluch
You should be able use nbviewer to look at your branches version (consider linking them in the PR like the colab links). If the rendering on nbviewer (what we link to in the readme) looks fine, don't worry about the formatting. I can imagine the ReviewNB view can make things a bit wonky sometimes. Please re-request a review when you're ready and I'll check things over again.

[bmeluch]

Both notebooks have been rerendered and are passing checks

NOM: Looks good in Github, nbviewer, Colab, and ReviewNB as far as I can see.

Taxonomy: Looks good in Github and Colab, text is weird in ReviewNB as noted, plots are weird in nbviewer. A mystery.

EDIT 10:30am FEB 11 NBVIEWER LOOKS NORMAL NOW HOORAY

[samobermiller]

Everything was generating fine for me other than the previously listed caveats in nbviewer!

[kheal]

huzzah! LGTM. Just make sure to change the link to the main branch in the first cell after it's been merged in - I forget the order of operations that @samobermiller had to do this, but I trust you two can figure it out.