Agents Instructions for anndataR

Project Overview

anndataR is a Bioconductor R package that provides native R support for reading/writing .h5ad (AnnData) files and bidirectional conversion between AnnData objects and popular Bioconductor/Seurat formats.

Key Features:

Native R reading/writing of .h5ad files (HDF5 backend)
Three AnnData implementations: InMemoryAnnData, HDF5AnnData, ReticulateAnnData
Bidirectional conversion: SingleCellExperiment ↔ AnnData ↔ Seurat
S4 coercion system for seamless type conversion
Python interoperability via reticulate

Architecture

R6 Class Hierarchy

AbstractAnnData (abstract base class)
├── InMemoryAnnData (all data in RAM)
├── HDF5AnnData (HDF5-backed, lazy loading)
├── ReticulateAnnData (Python anndata wrapper via reticulate)
└── AnnDataView (lazy subsetting view, no data copying)

When to use each:

InMemoryAnnData: Default for most operations, fast for small/medium datasets
HDF5AnnData: Large datasets exceeding RAM, on-disk persistence
ReticulateAnnData: Interoperability with Python anndata library, testing against Python behavior
AnnDataView: Lazy subsetting/slicing without copying data; convert to concrete implementation when needed

Core Slots (AnnData spec)

X: Main matrix (n_obs × n_vars)
layers: Named list of alternative matrices with same dimensions as X
obs: DataFrame with observation (cell) metadata (n_obs rows)
var: DataFrame with variable (gene) metadata (n_vars rows)
obsm: List of observation-aligned matrices (e.g., PCA, UMAP embeddings)
varm: List of variable-aligned matrices
obsp: List of observation pairwise matrices (e.g., cell-cell distances)
varp: List of variable pairwise matrices
uns: Unstructured metadata (arbitrary nested lists/dicts)

Important validation rules:

All matrices in X/layers must have same shape: [n_obs, n_vars]
Row names of obs/var define observation/variable names
obsm/varm matrices must align: first dimension matches n_obs/n_vars
obsp/varp must be square pairwise matrices

Critical Implementation Details

1. obs_names/var_names Architecture

obs_names and var_names are now stored separately from obs/var data.frames:

# InMemoryAnnData and HDF5AnnData store names separately
private$.obs_names  # Character vector of observation names
private$.var_names  # Character vector of variable names

# obs/var data.frames are stored WITHOUT rownames internally
private$.obs  # Data.frame with NULL rownames
private$.var  # Data.frame with NULL rownames

# Dimnames are added ON-THE-FLY when users access data
ad$obs        # Returns data.frame with rownames = obs_names
ad$X          # Returns matrix with dimnames from obs_names/var_names

Why this matters:

All matrix data (X, layers, obsm, varm, obsp, varp) is stored internally without dimnames
Dimnames are dynamically added via .add_matrix_dimnames() and .add_obsvar_dimnames() helper methods
This ensures consistency with Python anndata where obs/var names are separate from the data
When setting obs/var, extract rownames first if present, then strip them

Pattern for setters:

# Extract names before validation
if (!is.null(value) && has_row_names(value)) {
  private$.obs_names <- rownames(value)
  rownames(value) <- NULL
}
private$.obs <- private$.validate_obsvar_dataframe(value, "obs")

Use obs_names/var_names properties directly:

Don't use rownames(ad$obs) or colnames(ad$X) in internal code
Use ad$obs_names and ad$var_names for reliable access to names

2. AnnDataView for Lazy Subsetting

AnnDataView provides lazy subsetting without data copying:

# Create a view with S3 [ operator
ad <- AnnData(
  X = matrix(1:15, 3L, 5L),
  obs = data.frame(row.names = LETTERS[1:3], cell_type = c("A", "B", "A"))
)
view <- ad[ad$obs$cell_type == "A", ]  # Returns AnnDataView, no data copied

# Convert to concrete implementation when needed
result <- view$as_InMemoryAnnData()  # Now subsetting is applied

Key characteristics:

Inherits from AbstractAnnData
Stores base AnnData object and subset indices
All getters apply subsetting on-the-fly
Setters are disabled - must convert to concrete implementation first
Use .apply_subset() helper for matrix/data.frame subsetting
Use .apply_vector_subset() for vector subsetting (obs_names, var_names)

Testing pattern: See tests/testthat/test-AnnDataView.R for usage examples

3. S3 Methods for AbstractAnnData

Standard R S3 methods now work on all AnnData objects:

# Dimension methods
dim(ad)           # [n_obs, n_vars]
nrow(ad)          # n_obs
ncol(ad)          # n_vars
dimnames(ad)      # list(obs_names, var_names)
rownames(ad)      # obs_names
colnames(ad)      # var_names

# Subsetting with [ operator
ad[1:5, ]         # Subset observations, returns AnnDataView
ad[, 1:10]        # Subset variables, returns AnnDataView
ad[1:5, 1:10]     # Subset both, returns AnnDataView

Implementation: See R/AbstractAnnData-s3methods.R for all S3 methods

4. HDF5 File Management

Pattern: HDF5AnnData manages file handles with lifecycle:

# Automatic closure on finalization
adata <- read_h5ad("file.h5ad")  # close_on_finalize = TRUE

# Manual closure required for explicit construction
adata <- HDF5AnnData$new("file.h5ad")
adata$close()  # Must call explicitly

# Check validity before operations
private$.check_file_valid()  # Throws if handle closed

Testing pattern: test-h5ad-fileclosure.R validates handles close properly.

5. Validation Patterns

Alignment validation:

# All setters use validation helpers from AbstractAnnData
private$.validate_aligned_array(
  value,
  "X",
  shape = c(self$n_obs(), self$n_vars()),
  expected_rownames = rownames(self),
  expected_colnames = colnames(self)
)

Dimension checking:

private$.validate_aligned_mapping(
  value,
  "layers",
  c(self$n_obs(), self$n_vars()),
  expected_rownames = rownames(self),
  expected_colnames = colnames(self)
)

Testing Infrastructure

Conditional Test Skipping

Pattern: Helper functions check for optional dependencies:

# tests/testthat/helper-skip_if_no_anndata.R
skip_if_no_anndata <- function() {
  if (!rlang::is_installed("reticulate")) {
    skip("reticulate not installed")
  }
  
  # Check Python anndata module
  if (!reticulate::py_module_available("anndata")) {
    skip("Python anndata not available")
  }
}

# Usage in tests
test_that("ReticulateAnnData works", {
  skip_if_no_anndata()
  # ... test code ...
})

Available skip helpers:

skip_if_no_anndata(): Python anndata + reticulate
skip_if_no_dummy_anndata(): anndataR.testdata Python module (for roundtrip tests)
skip_if_no_h5diff(): h5diff CLI tool

Roundtrip Testing Pattern

Goal: Ensure R read/write matches Python anndata behavior

# tests/testthat/test-roundtrip-X.R example
test_that("Dense X roundtrips correctly", {
  skip_if_no_dummy_anndata()
  
  # Generate test data with known structure
  adata <- generate_dataset(
    X_type = "dense",
    obs = data.frame(row.names = LETTERS[1:10]),
    var = data.frame(row.names = letters[1:5])
  )
  
  # Write R → H5AD
  tmp <- tempfile(fileext = ".h5ad")
  adata$write_h5ad(tmp)
  
  # Read back and verify
  adata2 <- read_h5ad(tmp)
  expect_equal(adata$X, adata2$X)
  
  # Compare with Python via dummy_anndata
  py <- reticulate::import("anndataR.testdata")
  py_adata <- py$dummy_anndata(X = "dense")
  expect_equal_py(adata, py_adata)  # Custom helper
})

Custom helpers:

expect_equal_py(r_adata, py_adata): Compare R and Python AnnData objects
generate_dataset(): Create test AnnData with configurable matrix types

Mock Data Generation

Usage:

# R/generate_dataset.R
adata <- generate_dataset(
  X_type = "dense",           # "dense", "sparse", "csparse", "rsparse"
  obs = data.frame(row.names = LETTERS[1:100]),
  var = data.frame(row.names = letters[1:50]),
  n_layers = 2,
  obs_has_row_names = TRUE    # Toggle for testing edge cases
)

Conversion System

From External Formats

Pattern: from_*() functions for explicit conversion:

# from_SingleCellExperiment.R
adata <- from_SingleCellExperiment(
  sce,
  output_class = "InMemoryAnnData",  # or "HDF5AnnData"
  X_name = "counts",                  # Which assay → X
  layers = c("logcounts"),            # Additional assays → layers
  uns_keys = c("pca")                 # Which metadata → uns
)

# from_Seurat.R
adata <- from_Seurat(
  seurat_obj,
  output_class = "InMemoryAnnData",
  assay = "RNA"                       # Which assay to extract
)

Guessing pattern: from_Seurat() uses helper functions to intelligently map:

.from_Seurat_guess_layers(): Identify assay data slots
.from_Seurat_guess_obsms(): Extract dimensionality reductions (PCA, UMAP)
.from_Seurat_guess_uns(): Map miscellaneous metadata

To External Formats

Pattern: as_*() functions with optional parameters:

# as_SingleCellExperiment.R
sce <- as_SingleCellExperiment(
  adata,
  X_name = "counts",        # What to call X assay
  layer_names = NULL        # Which layers to include (NULL = all)
)

# as_Seurat.R
seurat <- as_Seurat(
  adata,
  assay_name = "RNA"        # Assay name in Seurat object
)

Development Workflow

Build and Test Commands

# Full R CMD check (Bioconductor standards)
R CMD build .
R CMD check --as-cran anndataR_*.tar.gz

# Quick test suite
R -e 'devtools::test()'

# Run specific test file
R -e 'devtools::test(filter = "roundtrip-X")'

# Lint checking
R -e 'lintr::lint_package()'

# Check code formatting
air format --check .

# Reformat code
air format .

Lintr Configuration

Key rules:

Line length: 120 characters max
Use paste() to wrap long strings in test helpers
Prefer explicit :: for package functions in examples

Example fix:

# ❌ Too long
expect_warning(as(adata, "Seurat"), "Consider using as_Seurat() for more control over the conversion")

# ✅ Wrapped
expect_warning(
  as(adata, "Seurat"),
  paste(
    "Consider using as_Seurat() for more control",
    "over the conversion"
  )
)

Dependency Management

Pattern: Check for optional packages before use:

# R/check_requires.R
check_requires <- function(package, reason = NULL) {
  if (!rlang::is_installed(package)) {
    msg <- c(
      "!" = "Package {.pkg {package}} is required",
      "i" = "Install with: {.code install.packages(\"{package}\")}"
    )
    if (!is.null(reason)) {
      msg <- c(msg, "i" = reason)
    }
    cli::cli_abort(msg)
  }
}

# Usage
as_Seurat <- function(adata, ...) {
  check_requires("SeuratObject", "for converting to Seurat objects")
  # ... conversion code ...
}

Common Pitfalls

1. obs_names/var_names Separation

Problem: Trying to access obs/var names via rownames instead of dedicated properties

Wrong:

# ❌ Internal code should not use this pattern
obs_ids <- rownames(adata$obs)
gene_ids <- colnames(adata$X)

Correct:

# ✅ Always use dedicated properties
obs_ids <- adata$obs_names
gene_ids <- adata$var_names

Why: obs_names/var_names are stored separately and added on-the-fly to user-facing data

2. Row Names Handling

Problem: R data.frames require unique row names, but AnnData allows duplicates

Solution: generate_dataframe.R has obs_has_row_names parameter for testing edge cases

3. Sparse Matrix Compatibility

Problem: Different sparse matrix classes (Matrix::dgCMatrix vs Matrix::dgRMatrix)

Solution: Use generate_dataset(X_type = "csparse") for CSC, "rsparse" for CSR testing

4. NULL vs Empty List in uns

Problem: Python distinguishes None from {}; R treats NULL differently

Solution: As of anndata 0.12.0, write NULL as empty HDF5 dataset. Controlled by options(anndataR.write_null = TRUE)

5. Closure Variable Capture in Factories

Problem: Loop variables not captured in closure

# ❌ WRONG - all handlers reference final iteration value
for (class in classes) {
  setAs(class, "Seurat", function(from) convert(from, class))
}

# ✅ CORRECT - force() captures variable value
.make_convert_handler <- function(convert_fn, from_str, to_str) {
  force(convert_fn)
  force(from_str)
  force(to_str)
  function(from) convert_fn(from)
}

File Organization

Source Files by Category

Core Classes:

R/AbstractAnnData.R: Base class with abstract slots and validation
R/AbstractAnnData-s3methods.R: S3 methods (dim, nrow, ncol, dimnames, [)
R/InMemoryAnnData.R: RAM-based implementation
R/HDF5AnnData.R: HDF5-backed implementation
R/ReticulateAnnData.R: Python wrapper (experimental)
R/AnnDataView.R: Lazy view for subsetting without data copying

I/O:

R/read_h5ad.R, R/read_h5ad_helpers.R: Reading HDF5 files
R/write_h5ad.R, R/write_h5ad_helpers.R: Writing HDF5 files
R/write_hdf5_helpers.R: Low-level HDF5 utilities

Conversion:

R/as-coercions.R: S4 coercion registration
R/as_AnnData.R: Generic converter to AnnData
R/as_SingleCellExperiment.R: AnnData → SCE
R/as_Seurat.R: AnnData → Seurat
R/from_SingleCellExperiment.R: SCE → AnnData
R/from_Seurat.R: Seurat → AnnData

Testing:

R/generate_dataset.R, R/generate_*.R: Mock data generation
tests/testthat/helper-*.R: Test utilities and skip helpers
tests/testthat/test-roundtrip-*.R: Python compatibility tests
tests/testthat/test-as-*.R: Conversion validation
tests/testthat/test-AnnDataView.R: Lazy subsetting tests
tests/testthat/test-AbstractAnnData-s3methods.R: S3 method tests

Utilities:

R/check_requires.R: Dependency validation
R/ui.R: CLI messaging helpers
R/utils.R: Miscellaneous helpers
R/known_issues.R: Track known bugs/limitations

Documentation Standards

Roxygen2 Patterns

Class documentation:

#' @title InMemoryAnnData
#' @description Implementation of an in-memory AnnData object.
#' @seealso [AnnData-usage] for details on creating and using AnnData objects
#' @family AnnData classes
#' @examples
#' adata <- AnnData(X = matrix(1:15, 3L, 5L), ...)

Cross-references:

Use [AnnData-usage] for user-facing documentation
Link related functions: @seealso [read_h5ad()], [write_h5ad()]

Vignettes

vignettes/anndataR.Rmd: Main usage guide
vignettes/software_design.Rmd: Architecture documentation
vignettes/usage_*.Rmd: Format-specific tutorials
vignettes/known_issues.Rmd: Documented limitations

CI/CD Considerations

Bioconductor requirements:

Must pass R CMD check --as-cran with no errors/warnings
BiocCheck compliance
All examples must run successfully
Conditional package usage (see check_requires pattern)

Quick Reference

Creating AnnData Objects

# In-memory (default)
adata <- AnnData(
  X = matrix(1:15, 3L, 5L),
  obs = data.frame(row.names = LETTERS[1:3]),
  var = data.frame(row.names = letters[1:5])
)

# HDF5-backed
adata <- HDF5AnnData$new("path.h5ad", mode = "w")
adata$X <- matrix(1:15, 3L, 5L)
# ... set other slots ...

# From file
adata <- read_h5ad("file.h5ad")

Conversion Examples

# SingleCellExperiment → AnnData
adata <- from_SingleCellExperiment(sce, X_name = "counts")

# AnnData → SingleCellExperiment
sce <- as_SingleCellExperiment(adata)

# Seurat → AnnData
adata <- from_Seurat(seurat_obj)

# AnnData → Seurat
seurat <- as_Seurat(adata)

# S4 coercion (if registered)
sce <- as(adata, "SingleCellExperiment")

Accessing Data

# Dimensions (using S3 methods)
dim(adata)         # [n_obs, n_vars]
nrow(adata)        # n_obs
ncol(adata)        # n_vars
dimnames(adata)    # list(obs_names, var_names)
rownames(adata)    # obs_names
colnames(adata)    # var_names

# Or using R6 methods
adata$n_obs()      # Number of observations
adata$n_vars()     # Number of variables

# Main matrix
adata$X            # Read
adata$X <- mat     # Write

# Metadata
adata$obs          # Observation metadata
adata$var          # Variable metadata
adata$uns          # Unstructured metadata

# Additional matrices
adata$layers[["raw"]]      # Named layer
adata$obsm[["X_pca"]]      # Observation matrix (PCA)
adata$obsp[["distances"]]  # Pairwise matrix

Subsetting with AnnDataView

# Subsetting returns AnnDataView (lazy, no data copied)
view <- adata[1:10, ]                     # Subset observations
view <- adata[, c("gene1", "gene2")]      # Subset variables
view <- adata[adata$obs$cell_type == "T", ]  # Conditional subsetting

# Convert to concrete implementation to apply changes
result <- view$as_InMemoryAnnData()
result <- view$as_HDF5AnnData("output.h5ad")

Questions to Ask When Contributing

Does this need Python compatibility? → Add roundtrip test
Requires optional package? → Use check_requires() + conditional tests
Modifying validation? → Check AbstractAnnData validators
New matrix type? → Add to generate_dataset() for testing
Changing uns handling? → Consider Python dict requirements
HDF5 changes? → Verify with h5diff against Python output
New conversion feature? → Update both from_*() and as_*() paths

Additional Resources

AnnData spec: Official Python documentation
vignettes/software_design.Rmd: Detailed architecture diagrams
inst/known_issues.yaml: Tracked bugs and workarounds
Bioconductor submission guidelines

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