H5ad helpers with pr83 #90
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- use `as.vector()` to reduce code duplication when reading nullable vectors - closes #82
- 'quietly' to suppress warnings; set to TRUE when relevant warnings are handled by calling code
- versions of rhdf5 that don't support ENUM; more user-friendly message - use to suppress irrelevant warnings in unit tests
* main: (26 commits) add gthb pat Update HDF5 writing functions and implement data frame writing (#85) remove shape trackstatus for now initial implementation of from_Seurat (#64) only check size when the names are already defined todo: add back obs_names and var_names length check update roxygen move required args to the front Update R/HDF5-read.R fix lint issues update tests refactor code to assume obs_names and var_names are defined Style and lint Add rhdf5 package skipe to HDF5 tests Add 1D sparse array to example.h5ad Remove requireNamespace("rhdf5") Fix bug in read_h5ad_string_array() Add support for reading H5AD rec arrays Covert 1D string arrays to vectors in read_h5ad_string_array() Update tests to use example.h5ad ...
…olean-enums' into h5ad-helpers-with-pr83
lazappi
approved these changes
Sep 1, 2023
| if (is.null(ordered)) { | ||
| attributes <- rhdf5::h5readAttributes(file, name) | ||
| ordered <- attributes[["ordered"]] | ||
| if (is.na(ordered)) { |
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Without any testing I think this might need to be is.null() (like in the original line)
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Hmm. Assuming attributes is a named list not containing the key ordered, that would make sense. However, when I change is.na(ordered) to is.null(ordered) and run the tests again, I get the following error:
Error (test-HDF5AnnData.R:32:3): reading obs works
Error in `if (ordered) "ordered"`: argument is not interpretable as logical
Backtrace:
▆
1. └─anndataR (local) `<fn>`() at test-HDF5AnnData.R:32:2
2. └─anndataR:::read_h5ad_element(private$.h5obj, "/obs", include_index = FALSE) at anndataR/R/HDF5AnnData.R:43:8
3. └─anndataR (local) read_fun(file = file, name = name, version = version, ...) at anndataR/R/HDF5-read.R:68:2
4. └─anndataR:::read_h5ad_collection(file, name, column_order) at anndataR/R/HDF5-read.R:369:2
5. └─anndataR:::read_h5ad_element(...) at anndataR/R/HDF5-read.R:424:4
6. └─anndataR (local) read_fun(file = file, name = name, version = version, ...) at anndataR/R/HDF5-read.R:68:2
7. └─base::factor(codes, labels = levels, ordered = ordered) at anndataR/R/HDF5-read
I can't even open the example hdf5 file:
> devtools::load_all()
> file <- system.file("extdata", "example.h5ad", package = "anndataR")
> adata <- HDF5AnnData$new(file)
> obs <- adata$obs
Error in if (ordered) "ordered" :
argument is not interpretable as logical
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When I add print(attributes) before the if-statement, I see:
> adata <- HDF5AnnData$new(file)
> adata
$`encoding-type`
[1] "categorical"
$`encoding-version`
[1] "0.2.0"
$ordered
[1] NA
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Going to assume is.na(ordered) is the correct condition. If we find out that ordered can sometimes be NULL as well, we can always add a second condition.
rcannood
added a commit
that referenced
this pull request
Sep 4, 2023
* Add read_h5ad function * Add read_h5ad tests * Add write_h5ad function * Move test dummy helper to main function Makes it possible to use for examples. Also add SingleCellExperiment and Seurat dummy functions. * Refactor dummy datasets into a single function Needs to be exported for examples * Add write_h5ad tests and examples * Style and lint * H5ad helpers ++ (#89) * Remove temporary workaround * use `inherits()` instead of `is()` * Add HDF5AnnData and InMemoryAnnData to `read_h5ad()` * fix incorrect merge * try to fix error in R devel * fix docs * add terminal newline * remove conditions * undo previous commit * H5ad helpers with pr83 (#90) * support rhdf5 nullable vector and boolean enum implementation - use `as.vector()` to reduce code duplication when reading nullable vectors - closes #82 * implement and use read_h5ad_attributes - 'quietly' to suppress warnings; set to TRUE when relevant warnings are handled by calling code * use 'anndataR-category-unknown' as a class of warning - versions of rhdf5 that don't support ENUM; more user-friendly message - use to suppress irrelevant warnings in unit tests * Tidy after merge and style * More tidying... * Roxygenise * Fix namespace --------- Co-authored-by: Martin Morgan <[email protected]> Co-authored-by: Luke Zappia <[email protected]> --------- Co-authored-by: Robrecht Cannoodt <[email protected]> Co-authored-by: Martin Morgan <[email protected]>
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Merges #83 into #88