Design • anndataR

anndataR is designed to offer the combined functionality of the following packages:

theislab/zellkonverter: Convert AnnData files to/from SingleCellExperiment objects.
mtmorgan/h5ad: Read/write *.h5ad files natively using rhdf5.
dynverse/anndata: An R implementation of the AnnData data structures, uses reticulate to read/write *.h5ad files.

Ideally, this package will be a complete replacement for all of these packages, and will be the go-to package for working with AnnData files in R.

Provide an R6 class to work with AnnData objects in R (either in-memory or on-disk).
Read/write *.h5ad files natively
Convert to/from SingleCellExperiment objects
Convert to/from Seurat objects

Here is a diagram of the main R6 classes provided by the package:

Notation:

X: Matrix - variable X is of type Matrix
*X: Matrix - variable X is abstract
to_SingleCellExperiment(): SingleCellExperiment - function to_SingleCellExperiment returns object of type SingleCellExperiment
*to_SingleCellExperiment() - function to_SingleCellExperiment is abstract

The following tables show the status of the implementation of each feature in the package:

AnnData

Slot	Getter	Getter test	Setter	Setter test
layers	NA	NA	NA	✓
obsm	NA	NA	NA	✓
varm	NA	NA	NA	✓
X	NA	NA	NA	✓

Slot	Getter	Getter test	Setter	Setter test
layers	✓	✓	✓	✓
obs	✓	✓	✓	✓
obs_names	✓	✓	✓	✓
obsm	✓		✓
obsp	✓		✓
uns	✓		✓
var	✓	✓	✓	✓
var_names	✓	✓	✓	✓
varm	✓		✓
varp	✓		✓
X	✓	✓	✓	✓

Slot	Getter	Getter test	Setter	Setter test
layers	✓	✓	✓	✓
obs	✓	✓	✓	✓
obs_names	✓	✓	✓	✓
obsm	✓		✓
obsp	✓		✓
uns	✓		✓
var	✓	✓	✓	✓
var_names	✓	✓	✓	✓
varm	✓		✓
varp	✓		✓
X	✓	✓	✓	✓

Slot	Getter	Getter test	Setter
layers	✓		✓
obs	✓	✓	✓
obs_names	✓	✓	✓
obsm	~		~
obsp	~		~
uns	✓		~
var	✓	✓	✓
var_names	✓	✓	✓
varm	~		~
varp	✓		~
X	✓		✓

Slot	Getter	Getter test	Setter	Setter test
layers	✓		✓	✓
obs	✓	✓	✓	✓
obs_names	✓	✓	✓	✓
obsm
obsp
uns
var	✓	✓	✓	✓
var_names	✓	✓	✓	✓
varm
varp
X	✓	✓	✓	✓