Add within-batch ARI plots to report template

[cbethell]

Issue Addressed Closes #354

What is the purpose of these changes?

The purpose of this PR is to add function implementation to calculate within-batch ARI values to the integration report, and to add the plots to display the calculated values.

What changes did you make?

A within-batch ARI plots section was added to the integration report template which implements the calculate_within_batch_ari() function from scpcaTools

Were there any other solutions that you tried?

Any comments, concerns, or questions important for reviewers Note: When trying to knit/run the template locally, I am receiving an error that object batch_ids cannot be found -- I tried adjusting the RemoteSha hash in the lock file to the latest commit for scpcaTools (which fixes the batch ids issue) but still receive the same error. I also tried running the setup_envs.sh script once again but that did not work. Any suggestions @allyhawkins @jashapiro?

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)

[cbethell]

I'm leaving some initial thoughts here. As far as the error, my only thought right now is deleting the conda folder like I mentioned in slack.

Thanks @allyhawkins, deleting the conda folder worked 🎉 I was able to implement the comments you left above as well.

Here's the example rendered report for reference: group01_integration_report.html.zip

[cbethell]

A few more small comments to address. The other thing I'm a little concerned about is that there looks to be two dots for each library with the exact same ari value? I think there should only be 1 value for each batch for each integration method correct?

Fixed the two dots issue by removing the additional geom_point() layer and also accounted for the cell_id_column argument that was added to the within-batch scpcaTools function 👍

For reference: group01_integration_report.html.zip