lamindb.core.MuDataCatManager¶

class lamindb.core.MuDataCatManager(mdata, var_index, categoricals=None, verbosity='hint', organism=None, sources=None, exclude=None)¶

Bases: CatManager

Curation flow for a MuData object.

Parameters:

mdata (MuData | Artifact) – The MuData object to curate.
var_index (dict[str, FieldAttr]) – The registry field for mapping the .var index for each modality. For example: {"modality_1": bt.Gene.ensembl_gene_id, "modality_2": CellMarker.name}
categoricals (dict[str, FieldAttr] | None, default: None) – A dictionary mapping .obs.columns to a registry field. Use modality keys to specify categoricals for MuData slots such as "rna:cell_type": bt.CellType.name".
verbosity (str, default: 'hint') – The verbosity level.
organism (str | None, default: None) – The organism name.
sources (dict[str, Record] | None, default: None) – A dictionary mapping .obs.columns to Source records.
exclude (dict | None, default: None) – A dictionary mapping column names to values to exclude from validation. When specific Source instances are pinned and may lack default values (e.g., “unknown” or “na”), using the exclude parameter ensures they are not validated.

Examples

>>> import bionty as bt
>>> curator = ln.Curator.from_mudata(
...     mdata,
...     var_index={
...         "rna": bt.Gene.ensembl_gene_id,
...         "adt": CellMarker.name
...     },
...     categoricals={
...         "cell_type_ontology_id": bt.CellType.ontology_id,
...         "donor_id": ULabel.name
...     },
...     organism="human",
... )

Attributes¶

property categoricals: dict¶: Return the obs fields to validate against.

property non_validated: dict[str, 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), verbosity='hint', organism=None, sources=None)¶

Return type:: AnnDataCatManager

classmethod from_df(df, categoricals=None, columns=FieldAttr(Feature.name), verbosity='hint', organism=None)¶

Return type:: DataFrameCatManager

classmethod from_mudata(mdata, var_index, categoricals=None, verbosity='hint', organism=None)¶

Return type:: MuDataCatManager

classmethod from_spatialdata(sdata, var_index, categoricals=None, organism=None, sources=None, exclude=None, verbosity='hint', *, sample_metadata_key='sample')¶

classmethod from_tiledbsoma(experiment_uri, var_index, categoricals=None, obs_columns=FieldAttr(Feature.name), organism=None, sources=None, exclude=None)¶

Return type:: TiledbsomaCatManager

Methods¶

add_new_from(key, modality=None, **kwargs)¶

Add validated & new categories.

Parameters:

key (str) – The key referencing the slot in the DataFrame.
modality (str | None, default: None) – The modality name.
organism – The organism name.
**kwargs – Additional keyword arguments to pass to create new records.

add_new_from_columns(modality, column_names=None, **kwargs)¶

add_new_from_var_index(modality, **kwargs)¶

Update variable records.

Parameters:

modality (str) – The modality name.
organism – The organism name.
**kwargs – Additional keyword arguments to pass to create new records.

lookup(public=False)¶

Lookup categories.

Parameters:: public (bool, default: False) – Perform lookup on public source ontologies.
Return type:: CurateLookup

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, modality=None)¶

Replace synonyms with standardized values.

Parameters:

key (str) – The key referencing the slot in the MuData.
modality (str | None, default: None) – The modality name.

Inplace modification of the dataset.

validate()¶

Validate categories.

Return type:: bool