lamindb.curators.AnnDataCatManager

class lamindb.curators.AnnDataCatManager(data, var_index=None, categoricals=None, obs_columns=FieldAttr(Feature.name), sources=None)

Bases: CatManager

Categorical manager for AnnData.

Attributes

property categoricals: dict

Return the obs fields to validate against.

property non_validated: dict[str, list[str]]

Return the non-validated features and labels.

property var_index: DeferredAttribute

Return the registry field to validate variables index against.

Class methods

classmethod from_anndata(data, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None)
Return type:

AnnDataCatManager

classmethod from_df(df, categoricals=None, columns=FieldAttr(Feature.name), organism=None)
Return type:

DataFrameCatManager

classmethod from_mudata(mdata, var_index, categoricals=None, organism=None)
Return type:

MuDataCatManager

classmethod from_spatialdata(sdata, var_index, categoricals=None, organism=None, sources=None, *, sample_metadata_key='sample')
classmethod from_tiledbsoma(experiment_uri, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None)
Return type:

TiledbsomaCatManager

Methods

add_new_from(key, **kwargs)

Add validated & new categories.

Parameters:

  • key (str) – The key referencing the slot in the DataFrame from which to draw terms.

  • **kwargs – Additional keyword arguments to pass to create new records

add_new_from_var_index(**kwargs)

Update variable records.

Parameters:

**kwargs – Additional keyword arguments to pass to create new records.

lookup(public=False)

Lookup categories.

Parameters:

public (bool, default: False) – If “public”, the lookup is performed on the public reference.

Return type:

CatLookup

save_artifact(*, key=None, description=None, revises=None, run=None)

Save an annotated artifact.

Parameters:

  • key (str | None, default: None) – A path-like key to reference artifact in default storage, e.g., "myfolder/myfile.fcs". Artifacts with the same key form a version family.

  • description (str | None, default: None) – A description.

  • revises (Artifact | None, default: None) – Previous version of the artifact. Is an alternative way to passing key to trigger a new version.

  • run (Run | None, default: None) – The run that creates the artifact.

Return type:

Artifact

Returns:

A saved artifact record.

standardize(key)

Replace synonyms with standardized values.

Parameters:

key (str) –

The key referencing the slot in adata.obs from which to draw terms. Same as the key in categoricals.

  • If “var_index”, standardize the var.index.

  • If “all”, standardize all obs columns and var.index.

Inplace modification of the dataset.

validate()

Validate categories.

This method also registers the validated records in the current instance.

Return type:

bool

Returns:

Whether the AnnData object is validated.