Analyze a sharded dataset

import lamindb as ln
import lnschema_bionty as lb

ln.track()

💡 loaded instance: testuser1/test-facs (lamindb 0.54.4)

💡 notebook imports: lamindb==0.54.4 lnschema_bionty==0.31.2 scanpy==1.9.5

💡 Transform(id='zzJzdgJ763Dyz8', name='Analyze a sharded dataset', short_name='facs3', version='0', type=notebook, updated_at=2023-10-01 16:44:53, created_by_id='DzTjkKse')

💡 Run(id='WFBzw6EMZ3lBgpeLPYfC', run_at=2023-10-01 16:44:53, transform_id='zzJzdgJ763Dyz8', created_by_id='DzTjkKse')

ln.Dataset.filter().df()

	name	description	version	hash	reference	reference_type	transform_id	run_id	file_id	initial_version_id	updated_at	created_by_id
id
8zlLWz5kwz4eVoYxBRwf	My versioned FACS dataset	None	1	Piw2n0vdnoNoAV7ZxgsW-g	None	None	OWuTtS4SAponz8	TJweM0VKGkTQHyy8CZci	8zlLWz5kwz4eVoYxBRwf	None	2023-10-01 16:44:34	DzTjkKse
8zlLWz5kwz4eVoYxBREt	My versioned FACS dataset	None	2	dmrCH-OEK94Zbh7i51wn	None	None	SmQmhrhigFPLz8	qh5Vw8DryjLToUWD3lqo	None	8zlLWz5kwz4eVoYxBRwf	2023-10-01 16:44:43	DzTjkKse

dataset = ln.Dataset.filter(name="My versioned FACS dataset", version="2").one()

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

/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/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.file_id.cat.categories

Index(['8zlLWz5kwz4eVoYxBRwf', 'rYTrXas2KdzpqLDUILvH'], dtype='object')

By default, the intersection of features is used:

adata.var.index

Index(['CD57', 'Cd19', 'Cd4', 'CD8', 'CD3', 'CD27', 'Cd14', 'Ccr7', 'CD127',
       'CD28'],
      dtype='object')

Let us create a plot:

markers = lb.CellMarker.lookup()

import scanpy as sc

sc.pp.pca(adata)
sc.pl.pca(adata, color=markers.cd14.name, save="_cd14")
filepath = "figures/pca_cd14"

WARNING: saving figure to file figures/pca_cd14.pdf

file = ln.File("./figures/pca_cd14.pdf", description="My result on CD14")

file.save()

file.view_flow()

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

💡 deleting instance testuser1/test-facs
✅     deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-facs.env

✅     instance cache deleted
✅     deleted '.lndb' sqlite file
❗     consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs

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