Convert to TRUE/FALSE mapping arguments
#274
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Pull Request Overview
This PR transitions conversion mapping arguments from NULL/empty lists to explicit TRUE/FALSE flags, where TRUE triggers default guessing and FALSE disables that slot. It updates core conversion functions, introduces a get_mapping helper, and refreshes vignettes, tests, and man pages to reflect the new API.
- Refactor: conversion functions now use
get_mapping(mapping, guesser, ...)with boolean defaults. - Documentation: vignettes and Rd files updated to show
TRUE/FALSEusage. - Tests: replaced legacy
from_Seuratcalls withas_AnnDataand adjusted mapping arguments.
Reviewed Changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/usage_singlecellexperiment.Rmd | Examples updated to use as_SingleCellExperiment and boolean mappings |
| vignettes/singlecellexperiment_mapping.Rmd | Revised narrative and examples for FALSE mapping; adjusted bullet points |
| vignettes/seurat_mapping.Rmd | Updated Seurat conversion examples to use FALSE mappings |
| tests/testthat/test-Seurat.R | Switched from from_Seurat to as_AnnData in tests |
| man/as_SingleCellExperiment.Rd | Changed default mapping args from NULL to TRUE |
| man/as_Seurat.Rd | Changed default mapping args from NULL to TRUE |
| man/as_AnnData.Rd | Changed default mapping args from NULL to TRUE |
| man/AbstractAnnData.Rd | Updated default mapping args and usage examples |
| R/utils.R | Added get_mapping() helper and its documentation |
| R/as.R | Refreshed commented examples to use boolean defaults |
| R/SingleCellExperiment.R | Refactored mapping logic to use get_mapping(); replaced simple with dataframe mapping |
| R/Seurat.R | Refactored mapping logic to use get_mapping() |
| R/AnnData.R | Updated generics and methods to use boolean defaults; changed signatures |
| R/AbstractAnnData.R | Updated R6 methods to default mapping args to TRUE |
Comments suppressed due to low confidence (1)
R/AnnData.R:247
- The
assay_nameparameter inas_AnnData.SingleCellExperimentwas changed to defaultTRUE, but it should remainNULL(or a character) to properly select which assay to map. Please revert it toNULL.
assay_name = TRUE,
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Update mapping arguments to use
TRUE/FALSEinstead ofNULL/c()TRUEuses the default guessed mappingFALSEmaps nothing for that slotFixes #268