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AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
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rOpenScPCA: plan notebook for cluster evaluation #775

Open sjspielman opened 1 week ago

sjspielman commented 1 week ago

Related to #727 & #731

This issue tracks planning the contents/scope of a template R notebook which can be used to evaluate clustering. The role of this notebook should be to present (visualize) quality metrics across group of clustering results so users can decide which set of clusters they might want to proceed with. Ideally, the template should be written flexibly enough so that it can also be used to just explore a single clustering result.

My initial thought is that users could generate this notebook with a function that takes two pieces of information: the results from sweep_clusters() and the SCE/Seurat object it came from. The reason for needing the full object is we'd probably like to visualize UMAP too, as people are generally interested in seeing this.

As part of planning this template, we should also identify functions we'll need to write for it.

jashapiro commented 1 week ago

Might it make sense to make this a template outside the R Package? I think that will make it more discoverable, as well as providing a practical example of using the package. I am also partly concerned about worrying too much about flexibility before we see how people might want to use this.