lamindb.core.AnnDataAnnotator¶
- class lamindb.core.AnnDataAnnotator(data, var_index, categoricals=None, using='default', verbosity='hint', organism=None)¶
Bases:
DataFrameAnnotator
Annotation flow for
AnnData
.- Parameters:
data (
AnnData
|str
|Path
) – The AnnData object or an AnnData-like path.var_index (
DeferredAttribute
) – The registry field for mapping the.var
index.categoricals (
dict
[str
,DeferredAttribute
] |None
, default:None
) – A dictionary mapping.obs.columns
to a registry field.using (
str
, default:'default'
) – A reference LaminDB instance.verbosity (
str
, default:'hint'
) – The verbosity level.organism (
str
|None
, default:None
) – The organism name.
Examples
>>> import bionty as bt >>> annotate = ln.Annotate.from_anndata( adata, var_index=bt.Gene.ensembl_gene_id, categoricals={"cell_type_ontology_id": bt.CellType.ontology_id, "donor_id": ln.ULabel.name}, organism="human", )
Attributes
- categoricals dict¶
Return the obs fields to validate against.
- fields dict¶
Return the columns fields to validate against.
- var_index FieldAttr¶
Return the registry field to validate variables index against.
Methods
- add_new_from_var_index(organism=None, **kwargs)¶
Update variable records.
- Parameters:
organism (
str
|None
, default:None
) – The organism name.**kwargs – Additional keyword arguments to pass to the registry model.
- lookup(using=None)¶
Lookup categories.
- Parameters:
using (
str
|None
, default:None
) – The instance where the lookup is performed. if None (default), the lookup is performed on the instance specified in “using” parameter of the validator. if “public”, the lookup is performed on the public reference.- Return type:
- save_artifact(description=None, **kwargs)¶
Save the validated
AnnData
and metadata.- Parameters:
description (
str
|None
, default:None
) – Description of theAnnData
object.**kwargs – Object level metadata.
- Return type:
- Returns:
A saved artifact record.
- validate(organism=None)¶
Validate categories.
- Parameters:
organism (
str
|None
, default:None
) – The organism name.- Return type:
bool
- Returns:
Whether the AnnData object is validated.