Add iLISI visualization to integration report

[cbethell]

Please provide some background on the proposed additions or changes.

After initiating the html report in the optional-integration-analysis module (#351), we will want to add plots showing the iLISI performance metric output on the unintegrated and integrated data.

What are the changes that you are proposing?

There should be an "integration performance" section of the data integration report template, and this should start with the iLISI performance metric.

Please describe the proposed solution.

An "iLISI" section should be added to the integration-report-template.Rmd with the following:

• steps to source or run a utils function specific to calculating iLISI
• a plot showing the iLISI values for each of the datasets (unintegrated and integrated)

I do not believe we want to source a script from another repo so we will want to add a script in utils that has function(s) for calculating iLISI like in the sc-data-integration repo: https://github.com/AlexsLemonade/sc-data-integration/blob/main/scripts/utils/calculate-LISI.R

[allyhawkins]

One thing I'm thinking about here is if we actually want to port over the functions for calculating this metric and the other metrics to scpcaTools before adding them into this report. Eventually we may want to use at least some of these metrics in an integration report for ScPCA so I think it makes sense to spend some time getting those functions in a single place we can utilize across multiple repos before we add in plots here.

[cbethell]

One thing I'm thinking about here is if we actually want to port over the functions for calculating this metric and the other metrics to scpcaTools before adding them into this report. Eventually we may want to use at least some of these metrics in an integration report for ScPCA so I think it makes sense to spend some time getting those functions in a single place we can utilize across multiple repos before we add in plots here.

👍 I can file an issue for this in the scpcaTools repo

[allyhawkins]

👍 I can file an issue for this in the scpcaTools repo

Thank you! Can you file one for each of the metrics we have? iLISI, ARI, ASW, and then within-batch ARI?