bioalpha.h5ad_map.SparseDatasetMap.as_format

SparseDatasetMap.as_format(spformat: Literal['csr', 'csc'], file: H5ADMapFile, key: str | None = None, force: bool = False)

Convert backed sparse matrix to other format without load full matrix to memory.

Parameters:

• spformat ("csr" | "csc") – Format that will convert to. If spformat == self.format_str, do nothing.

• file (h5py.File) – Output handle that backed matrix will saved on.

• key (str, default = None) – Key saved to file. Default is spformat.

Returns:

spmatrix – Converted backed sparse matrix.

Return type:

SparseDatasetMap

Examples

>>> with H5ADMap("matrix.h5ad") as adata:
...   adata.X.as_format("csc", adata.layers)
...   print(adata)

AnnData object with n_obs x n_vars = 1751246 x 45526 backed at “./matrix.h5ad”

layers: “csc”