sfaira.data.Universe.streamline_metadata

Universe.streamline_metadata(schema: str = 'sfaira', clean_obs: bool = True, clean_var: bool = True, clean_uns: bool = True, clean_obs_names: bool = True, keep_orginal_obs: bool = False, keep_symbol_obs: bool = True, keep_id_obs: bool = True)

Streamline the adata instance in each group and each data set to output format. Output format are saved in ADATA_FIELDS* classes.

Parameters

• schema – Export format. - “sfaira” - “cellxgene”

• clean_obs – Whether to delete non-streamlined fields in .obs, .obsm and .obsp.

• clean_var – Whether to delete non-streamlined fields in .var, .varm and .varp.

• clean_uns – Whether to delete non-streamlined fields in .uns.

• clean_obs_names – Whether to replace obs_names with a string comprised of dataset id and an increasing integer.

• clean_obs_names – Whether to replace obs_names with a string comprised of dataset id and an increasing integer.

• keep_orginal_obs – For ontology-constrained .obs columns, whether to keep a column with original annotation.

• keep_symbol_obs – For ontology-constrained .obs columns, whether to keep a column with ontology symbol annotation.

• keep_id_obs – For ontology-constrained .obs columns, whether to keep a column with ontology ID annotation.

Returns