Conversion from & to SingleCellExperiment #212
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rcannood
reviewed
Feb 6, 2025
R/SingleCellExperiment.R
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| col_data_mapping = NULL, | ||
| row_data_mapping = NULL, | ||
| reduction_mapping = NULL, | ||
| colPairs_mapping = NULL, # nolint | ||
| rowPairs_mapping = NULL, # nolint |
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why is col_data_mapping snakecase but colPairs_mapping camelcase?
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Good point, no reason and we should be consistent.
vignettes/singlecellexperiment.Rmd
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Could this vignette be renamed to detailed_singlecellexperiment or something like this?
Also, could you add an entry to _pkgdown.yml?
rcannood
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Feb 6, 2025
vignettes/singlecellexperiment.Rmd
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| ```{r construct_anndata} | ||
| library(anndataR) | ||
| library(SingleCellExperiment) | ||
|
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Suggested change
| ```{r construct_anndata} | |
| library(anndataR) | |
| library(SingleCellExperiment) | |
| ```{r deps, message=FALSE, warning=FALSE} | |
| library(anndataR) | |
| library(SingleCellExperiment) | |
| ``` | |
| We first generate a sample dataset to work with. | |
| ```{r construct_anndata} |
|
Minor comments, otherwise LGTM! |
rcannood
approved these changes
Feb 6, 2025
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Provides modular conversion to & from SingleCellExperiment.
Adds vignette explaining the mapping in detail.
Aims to follow some of the mapping of the Seurat conversion.