anndict.adata_dict.concatenate_adata_dict

anndict.adata_dict.concatenate_adata_dict(adata_dict, *, new_col_name=None, lower_peak_memory=False, **kwargs)

Concatenate all AnnData objects in adata_dict into a single AnnData object. If only a single AnnData object is present, return it as is.

Parameters:

adata_dict AdataDict

AdataDict

new_col_name str | None (default: None)

If provided, the name of the new column that will store the adata_dict key in .obs of the concatenated AnnData. Defaults to None.

lower_peak_memory bool (default: False)

If True, the the function concatenates the AnnData objects in adata_dict sequentially, and deletes the data from adata_dict as it does so. This reduces peak memory usage.

kwargs

Additional keyword arguments for concatenation.

Return type:

AnnData

Returns:

A single AnnData object. The .obs will contain a new column specifying the key of the AnnData of origin.

Raises:

ValueError – If adata_dict is empty.

Warning

lower_peak_memory defaults to False. If lower_peak_memory is set to True, adata_dict will be deleted during the concatenation process.

Notes

Memory is only freed if no other references to the AnnData objects in adata_dict exist.