lamindb.examples.ingest_mini_immuno_datasets¶
- lamindb.examples.ingest_mini_immuno_datasets()¶
Ingest mini immuno datasets.
import lamindb as ln import bionty as bt # observation-level metadata ln.Feature(name="perturbation", dtype="cat[ULabel]").save() ln.Feature(name="sample_note", dtype="str").save() ln.Feature(name="cell_type_by_expert", dtype="cat[bionty.CellType]").save() ln.Feature(name="cell_type_by_model", dtype="cat[bionty.CellType]").save() # dataset-level metadata ln.Feature(name="temperature", dtype="float").save() ln.Feature(name="experiment", dtype="cat[ULabel]").save() ln.Feature(name="date_of_study", dtype="date").save() ln.Feature(name="study_note", dtype="str").save() ln.Feature(name="study_metadata", dtype=dict).save() ## Permissible values for categoricals ln.ULabel.from_values(["DMSO", "IFNG"], create=True).save() ln.ULabel.from_values(["Experiment 1", "Experiment 2"], create=True).save() bt.CellType.from_values(["B cell", "T cell"], create=True).save() schema = ln.examples.schemas.anndata_ensembl_gene_ids_and_valid_features_in_obs() ## Ingest dataset1 adata = ln.core.datasets.mini_immuno.get_dataset1(otype="AnnData") artifact = ln.Artifact.from_anndata( adata, key="examples/dataset1.h5ad", schema=schema, ).save() adhoc = {"study_metadata": {"detail1": "123", "detail2": 1}} dataset_metadata = adata.uns dataset_metadata.update(adhoc) artifact.features.add_values(dataset_metadata) # Ingest dataset2 adata2 = ln.core.datasets.mini_immuno.get_dataset2(otype="AnnData") artifact2 = ln.Artifact.from_anndata( adata2, key="examples/dataset2.h5ad", schema=schema, ).save() adhoc2 = {"study_metadata": {"detail1": "456", "detail2": 2}} dataset_metadata2 = adata2.uns dataset_metadata2.update(adhoc2) artifact2.features.add_values(dataset_metadata2)