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Add cell_type_mapper implementation of correlation mapping #36

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jeremymiller opened this issue Dec 21, 2024 · 0 comments
Open

Add cell_type_mapper implementation of correlation mapping #36

jeremymiller opened this issue Dec 21, 2024 · 0 comments
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@jeremymiller
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Add a 5th mapping option in taxonomy_mapping, which is the flat version of cell_type_mapper. The steps below are a starting point for how one could do this. Inkar may have a better way.

  • Precalculate a second set statistics for a flat hierarchy (e.g., only “cluster_label”)
  • Store these stats in a slot called AIT_anndata$uns$hierarchical[[mode_cor]] where mode_cor = [mode]_correlation (not ideal but for back compatibility and to minimize code updates)
  • Update taxonomy_mapping with a new parameter called “flat.map” that stores this version of correlation mapping and that calls cell_type_mapper with this new mode and the flat hierarchy when flat.map=TRUE
  • Update documentation for taxonomy_mapping to describe the differences in all the mappings better (specifically in the header above the function, then call roxygen2::oxygenize() or however you do it).
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