opendvp.io.export_adata

export_adata(adata, path_to_dir, checkpoint_name, export_as_cvs=False, metadata_cols=None, metadata_index=None, parquet=False, perseus=False)

Save an AnnData object as both .h5ad and optionally .parquet, .csv, or Perseus files in a checkpoint directory.

Return type:

None

Parameters:

adataAnnData

AnnData object to save.

path_to_dirstr

Directory where the checkpoint folder will be created.

checkpoint_namestr

Name for the checkpoint folder and file prefix.

export_as_cvsbool, optional

If True, exports the data and metadata as .csv (tab-delimited) or .parquet files. Default is False.

metadata_colslist, optional

List of columns from adata.obs to include in the metadata file. If None, all columns are included.

metadata_indexstr, optional

Column from adata.obs to use as index in the exported files. If None, uses the default index.

parquetbool, optional

If True, exports as .parquet files instead of .csv. Only used if export_as_cvs is True.

perseusbool, optional

If True, exports Perseus-compatible files in a subfolder. Default is False.

Returns:

None

This function saves files to disk and does not return a value.

Example:

>>> from opendvp.io.export_adata import export_adata
>>> import anndata as ad
>>> import numpy as np
>>> import pandas as pd
>>> X = np.random.rand(10, 5)
>>> obs = pd.DataFrame({"celltype": ["A"] * 5 + ["B"] * 5}, index=[f"cell{i}" for i in range(10)])
>>> var = pd.DataFrame(index=[f"gene{i}" for i in range(5)])
>>> adata = ad.AnnData(X=X, obs=obs, var=var)
>>> export_adata(adata, path_to_dir="checkpoints", checkpoint_name="test", export_as_cvs=True, perseus=True)