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', loadAnnDatainbackedmode instead of fully loading it into memory (memorymode). If you want to modify backed attributes of the AnnData object, you need to choose'r+'.- as_sparse :
Sequence[str] (default:()) If an array was saved as dense, passing its name here will read it as a sparse_matrix, by chunk of size
chunk_size.- as_sparse_fmt :
Type[spmatrix] (default:<class 'scipy.sparse.csr.csr_matrix'>) Sparse format class to read elements from
as_sparsein as.- chunk_size :
int(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.
- filename :
- Return type