Analyze the collection and save a result

import lamindb as ln
import bionty as bt

ln.settings.transform.stem_uid = "zzJzdgJ763Dy"
ln.settings.transform.version = "0"
ln.track()

💡 connected lamindb: testuser1/test-facs

💡 notebook imports: bionty==0.42.9 lamindb==0.71.0 scanpy==1.10.1

💡 saved: Transform(uid='zzJzdgJ763Dy6K79', name='Analyze the collection and save a result', key='facs4', version='0', type='notebook', updated_at=2024-05-01 18:53:44 UTC, created_by_id=1)

💡 saved: Run(uid='KobnPcvEDksHkySSan8m', transform_id=4, created_by_id=1)

ln.Collection.df()

	uid	name	description	version	hash	reference	reference_type	transform_id	run_id	artifact_id	visibility	created_at	updated_at	created_by_id
id
2	HTrdwbAlVOM0WX6aPw80	My versioned cytometry collection	None	2	aIyjTZDm9LEyi4udLlQ-	None	None	2	2	None	1	2024-05-01 18:53:34.248736+00:00	2024-05-01 18:53:34.248760+00:00	1
1	HTrdwbAlVOM0WX6aNptu	My versioned cytometry collection	None	1	_SSVHoSL17yyiRlHc8Hr	None	None	1	1	None	1	2024-05-01 18:53:23.402360+00:00	2024-05-01 18:53:23.402386+00:00	1

collection = ln.Collection.filter(
    name="My versioned cytometry collection", version="2"
).one()

adata = collection.load(join="inner")

/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/anndata/_core/anndata.py:1838: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")

The AnnData has the reference to the individual files in the .obs annotations:

adata.obs.artifact_uid.cat.categories

Index(['xRZvdCScS4EGAOaS8uak', 'TPjJBPzyNCizdD52cNIE'], dtype='object')

By default, the intersection of features is used:

adata.var.index

Index(['CD8', 'CD27', 'Ccr7', 'Cd4', 'CD45RA', 'CD3'], dtype='object')

Let us create a plot:

markers = bt.CellMarker.lookup()

import scanpy as sc

sc.pp.pca(adata)
sc.pl.pca(adata, color=markers.cd8.name, save="_cd8")

WARNING: saving figure to file figures/pca_cd8.pdf

artifact = ln.Artifact("./figures/pca_cd8.pdf", description="My result on CD8")

artifact.save()

Artifact(uid='EWywqiIAPBuLIeJbs7Vv', suffix='.pdf', description='My result on CD8', size=5622580, hash='3M-ppRjmxfCIGaIFq-QpjQ', hash_type='md5', visibility=1, key_is_virtual=True, updated_at=2024-05-01 18:54:02 UTC, storage_id=1, transform_id=4, run_id=4, created_by_id=1)

artifact.view_lineage()

Given the image is part of the notebook, there isn’t an actual need to save it and you can also rely on the report that you’ll create when saving the notebook via the command line via:

lamin save <notebook_path>

# clean up test instance
!lamin delete --force test-facs
!rm -r test-flow

Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/lamin", line 8, in <module>
    sys.exit(main())
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 360, in __call__
    return super().__call__(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamin_cli/__main__.py", line 103, in delete
    return delete(instance, force=force)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/_delete.py", line 140, in delete
    n_objects = check_storage_is_empty(
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/core/upath.py", line 814, in check_storage_is_empty
    raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage /home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb contains 4 objects ('./lamindb/_is_initialized'  ignored) - delete them prior to deleting the instance
['/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb/EWywqiIAPBuLIeJbs7Vv.pdf', '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb/TPjJBPzyNCizdD52cNIE.h5ad', '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb/_is_initialized', '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb/xRZvdCScS4EGAOaS8uak.h5ad']

rm: cannot remove 'test-flow': No such file or directory