Initiate GOI module README

[cbethell]

What is the purpose of these changes?

This PR initiates the genes of interest (GOI) module documentation.

What changes did you make?

A README.md file is added to the optional-goi-analysis module here, so far with just an analysis overview section along with expected input and expected output.

Any comments, concerns, or questions important for reviewers

• Is there any additional information you feel should be added here (keeping in mind that documentation referencing parameters and how to run workflow will be in a subsequent PR)?

Checklist

Place an x in all boxes that you have completed.

• I have run the most recent version of the code
• If I am adding in reports or generating any plots, I have reviewed the necessary reports
• I have added all necessary documentation (if applicable)

[allyhawkins]

I took a first look and added some general comments. The biggest comment is about the overview of the actual workflow. We should describe the actual steps that are taken in the workflow rather then just the two scripts that are run.

[allyhawkins]

I think it would make more sense to break these steps up into something that makes more sense to external users and not just the two steps that we do which is calculations and plots. What actually is happening in the script?

Maybe something like these headers?

1. Mapping gene identifiers
2. Heirarchical clustering of dataset with genes of interest - this is what the heatmap represents
3. Visualization of genes of interest expression (Sina, PCA, and UMAP)

[cbethell]

All good points @allyhawkins! I've re-structured the analysis overview headers, added a code chunk with the tree structure of the output, re-arranged some wording per the recent updates we made -- let me know what you think of things now!

[allyhawkins]

Thanks for making these changes! I think there will still be some things we don't have fully fleshed out yet, but this mostly looks good. I think the biggest question I have is how we want to deal with explaining mapping gene identifiers.

[allyhawkins]

I think this might change when we get to the snakefile, as it would make sense to move the rendered html file out of the goi_stats folder, but this is fine for now.

[cbethell]

Thanks for the review @allyhawkins, I implemented those wording changes and will file an issue regarding a separate section to explain mapping gene identifiers. Otherwise let me know what you think now 👍

[allyhawkins]

Looks good! One more minor change but I don't need to see it again.