AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
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rOpenScPCA: function to calculate silhouette width #771

Closed sjspielman closed 1 month ago

sjspielman commented 1 month ago

Relevant discussions

https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/727 & https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/731

Proposed addition

This issue tracks adding a function and associated tests to rOpenScpCA to calculate silhouette width from a given set of clusters. The function should take a PC matrix (or sce/seurat object) and data frame with clusters and cell IDs. The function should return an updated cluster data from with silhouette width values. Note that calculating average silhouette width is not something this function will do; that will be in a future function to summarize/visualize stats.

sjspielman commented 1 month ago

Closed by #777