This PR adds two functions - calculating silhouette width and calculating neighhorhood purity - to rOpenScPCA. These functions are pretty parallel in scope, but if there is a different strategy (like, inputs/output formats) you want to recommend let me know. I also left a few TODO comments in the code which you'll see when reviewing - one about how much bluster output to return, and one about testing.
I also ended up splitting out that matrix checking code into its own function, since I used that code as part of these functions too. I didn't add any explicit tests for that helper function so it's implicitly tested all over the place, but I can, e.g., maybe change over some extract_pc_matrix tests to focus on prepare_pc_matrix if we want something explicit here.
Closes #771 Closes #772
This PR adds two functions - calculating silhouette width and calculating neighhorhood purity - to rOpenScPCA. These functions are pretty parallel in scope, but if there is a different strategy (like, inputs/output formats) you want to recommend let me know. I also left a few
TODOcomments in the code which you'll see when reviewing - one about how much bluster output to return, and one about testing.I also ended up splitting out that matrix checking code into its own function, since I used that code as part of these functions too. I didn't add any explicit tests for that helper function so it's implicitly tested all over the place, but I can, e.g., maybe change over some
extract_pc_matrixtests to focus onprepare_pc_matrixif we want something explicit here.