[r] Add drop_levels to SOMAExperimentAxisQuery -> ecosystem outgestors
#2825
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…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$.load_df()` for loading `obs` and `var`; removing standalone code and increase sharing with the SCE outgestor resolves #2765 [SC-51945](https://app.shortcut.com/tiledb-inc/story/51945)
| @@ -515,6 +515,7 @@ SOMAExperimentAxisQuery <- R6::R6Class( | |||
| #' @param obsm_layers \Sexpr[results=rd]{tiledbsoma:::rd_outgest_mlayers()} | |||
| #' @param varm_layers \Sexpr[results=rd]{tiledbsoma:::rd_outgest_mlayers(axis = 'varm')} | |||
| #' @param obsp_layers \Sexpr[results=rd]{tiledbsoma:::rd_outgest_players()} | |||
| #' @param drop_levels Drop unused levels from \code{obs} and \code{var} factor columns | |||
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I do not use these patterns when I write docs so pardon the naive question but why do all other params here follow a pattern and this one doesn't?
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The previous ones used \Sexpr for templated docs that are similar but with minor variations between different methods as @template does not work with R6; however, the use of \Sexpr is the cause of the "installing package to process help pages" step when building tiledbsoma-r from source. As this step has been a source of complaint, I've resorted to copy-pasting docs and will eventually switch out all \Sexpr to copy-pasted docs to make building tiledbsoma-r easier
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I am 100% on board with the simplification and robustification.
Bump develop version [ci skip]
mojaveazure
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paulhoffman/sc-51945/to-seurat-and-to-single-cell-experiment-need
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R analog of #2811 and single-cell-data/SOMA#204; add a
drop_levelsparamter to the ecosystem outgestors to drop unused factor levels from resulting data framesModified SOMA methods:
SOMAExperimentAxisQuery$to_seurat(): adddrop_levelsto drop drop unused levels fromobsandvardata framesSOMAExperimentAxisQuery$to_seurat_assay(): adddrop_levelsto drop unused levels fromvardata frameSOMAExperimentAxisQuery$to_single_cell_experiment(): adddrop_levelsto drop unused levels fromobsandvardata framesAlso shifts
SOMAExperimentAxisQuery$to_seurat()andSOMAExperimentAxisQuery$to_seurat_assay()to useSOMAExperimentAxisQuery$private$.load_df()for loadingobsandvar; removing standalone code and increase sharing with the SCE outgestorresolves #2765
SC-51945