anndata.read_h5ad

anndata.read_h5ad(filename, backed=None, *, as_sparse=(), as_sparse_fmt=<class 'scipy.sparse.csr.csr_matrix'>, chunk_size=6000)

Read .h5ad-formatted hdf5 file.

Parameters
filename : str, PathUnion[str, Path]

File name of data file.

backed : {‘r’, ‘r+’}, bool, NoneUnion[Literal[‘r’, ‘r+’], bool, None] (default: None)

If 'r', load AnnData in backed mode instead of fully loading it into memory (memory mode). If you want to modify backed attributes of the AnnData object, you need to choose 'r+'.

as_sparse : Sequence[str]Sequence[str] (default: ())

If an array was saved as dense, passing it’s name here will read it as a sparse_matrix, by chunk of size chunk_size.

as_sparse_fmt : Type[spmatrix]Type[spmatrix] (default: <class 'scipy.sparse.csr.csr_matrix'>)

Sparse format to read elements from as_sparse in as.

chunk_size : intint (default: 6000)

Used only when loading sparse dataset that is stored as dense. Loading iterates through chunks of the dataset of this row size until it reads the whole dataset. Higher size means higher memory consumption and higher (to a point) loading speed.

Return type

AnnDataAnnData