Analyze the collection and save a result

import lamindb as ln
import bionty as bt

ln.track("zzJzdgJ763Dy0000")

→ connected lamindb: testuser1/test-facs

! creating spaces manually on sqlite databases is possible for demo purposes, but does *not* affect access permissions

→ created Transform('zzJzdgJ763Dy0000'), started new Run('FcDufflA...') at 2025-09-10 09:02:22 UTC

→ notebook imports: bionty==1.7a1 lamindb==1.11a1 scanpy==1.11.4

ln.Collection.to_dataframe()

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	uid	key	description	hash	reference	reference_type	space_id	meta_artifact_id	version	is_latest	run_id	created_at	created_by_id	_aux	branch_id
id
2	v9w35huBFEcJBp0d0001	My versioned cytometry collection	None	eNSQbRNsjg278G1RwXmqCw	None	None	1	None	2	True	2	2025-09-10 09:02:14.240000+00:00	1	None	1
1	v9w35huBFEcJBp0d0000	My versioned cytometry collection	None	jZ8YvUdZGRwPgfoBQbOg_Q	None	None	1	None	1	False	1	2025-09-10 09:02:04.377000+00:00	1	None	1

collection = ln.Collection.get(key="My versioned cytometry collection", version="2")

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

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! creating spaces manually on sqlite databases is possible for demo purposes, but does *not* affect access permissions

/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/anndata/_core/anndata.py:1774: 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

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Index(['BUrhruYi8Gw3rCVR0000', 'd1MS9a3t7v4yzBTB0000'], dtype='object')

By default, the intersection of features is used:

adata.var.index

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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")

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WARNING: saving figure to file figures/pca_cd8.pdf

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

! creating spaces manually on sqlite databases is possible for demo purposes, but does *not* affect access permissions

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:

ln.finish()

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

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

╭─ Error ──────────────────────────────────────────────────────────────────────╮
│ '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb'    │
│ contains 3 objects - delete them prior to deleting the storage location      │
╰──────────────────────────────────────────────────────────────────────────────╯