Drop unused categories in ExperimentAxisQuery.to_anndata
#204
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johnkerl
requested changes
Jul 24, 2024
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From the discussion here
single-cell-data/TileDB-SOMA#2765 (comment)
we need a new flag on to_anndata:
- optional
- default if omitted: current behavior
- if supplied and
True: do what this PR does - name:
droplevels? Or something else? Let's chat with @pablo-gar @mojaveazure @eddelbuettel
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As placeholder I have chosen |
johnkerl
reviewed
Jul 24, 2024
| @@ -298,7 +299,7 @@ def to_anndata( | |||
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Let's add a description of what drop_levels does ...
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@pablo-gar @eddelbuettel @mojaveazure are you okay with drop_levels?
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(Presuming we'll want a same-ish name in Python & R both ...)
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Seurat uses drop to match R, but I'm fine with drop_levels in SOMA
johnkerl
approved these changes
Jul 24, 2024
Co-authored-by: John Kerl <[email protected]>
mojaveazure
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Aug 2, 2024
…stors R analog of #2811 and single-cell-data/SOMA#204; add a `drop_levels` paramter to the ecosystem outgestors to drop unused factor levels from resulting data frames Modified SOMA methods: - `SOMAExperimentAxisQuery$to_seurat()`: add `drop_levels` to drop drop unused levels from `obs` and `var` data frames - `SOMAExperimentAxisQuery$to_seurat_assay()`: add `drop_levels` to drop unused levels from `var` data frame - `SOMAExperimentAxisQuery$to_single_cell_experiment()`: add `drop_levels` to drop unused levels from `obs` and `var` data frames Also shifts `SOMAExperimentAxisQuery$to_seurat()` and `SOMAExperimentAxisQuery$to_seurat_assay()` to use `SOMAExperimentAxisQuery$private$.load_df()` for loading `obs` and `var`; removing standalone code and increase sharing with the SCE outgestor resolves #2765 [SC-51945](https://app.shortcut.com/tiledb-inc/story/51945)
mojaveazure
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Aug 2, 2024
…stors (#2825) * [r] Add `drop_levels` to `SOMAExperimentAxisQuery` -> ecosystem outgestors R analog of #2811 and single-cell-data/SOMA#204; add a `drop_levels` paramter to the ecosystem outgestors to drop unused factor levels from resulting data frames Modified SOMA methods: - `SOMAExperimentAxisQuery$to_seurat()`: add `drop_levels` to drop drop unused levels from `obs` and `var` data frames - `SOMAExperimentAxisQuery$to_seurat_assay()`: add `drop_levels` to drop unused levels from `var` data frame - `SOMAExperimentAxisQuery$to_single_cell_experiment()`: add `drop_levels` to drop unused levels from `obs` and `var` data frames Also shifts `SOMAExperimentAxisQuery$to_seurat()` and `SOMAExperimentAxisQuery$to_seurat_assay()` to use `SOMAExperimentAxisQuery$private$.load_df()` for loading `obs` and `var`; removing standalone code and increase sharing with the SCE outgestor resolves #2765 [SC-51945](https://app.shortcut.com/tiledb-inc/story/51945) * Update changelog Bump develop version
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Issue:
single-cell-data/TileDB-SOMA#2765
Changes:
ExperimentAxisQuery.to_anndataiterates through each column and drops unused categories.Notes for Reviewer:
This change was originally proposed in single-cell-data/TileDB-SOMA#2811 but was suggested somacore was a more appropriate location for it.