Initiate data integration report template

[cbethell]

Issue Addressed Closes #351

What is the purpose of these changes?

This PR initiates the data integration report template.

What changes did you make?

A integration-report-template.Rmd file was added to the optional-integration-analysis module. This template currently contains the following:

• a breakdown of number of batches and number of cells per batch
• UMAPs for each of the integration methods being compared (including unintegrated)

Were there any other solutions that you tried?

It looks like we may need to tweak the perform-integration.R script here as well, as I tried running the template using both "fastMNN, harmony" as the integration methods but only the harmony results were found in the integrated SCE object

Any comments, concerns, or questions important for reviewers

• Does this tackle #351 as you would expect?

Checklist

Place an x in all boxes that you have completed.

• [x] 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)

[cbethell]

Okay I added the perform_dim_reduction() function as we discussed @allyhawkins and that fixed the missing dimension reduction results issue -- here is a zip of the rendered html as it currently is: integration-report-template.html.zip

[cbethell]

Implemented those comments you left @allyhawkins, thank you! I also successfully tested the gt package installation in the report template as we discussed 👍

[cbethell]

Added that function documentation and removed those extra libraries that were being loaded in -- let me know what you think now @allyhawkins!