Analyze a dataset in memory

Here, we’ll analyze the growing dataset by loading it into memory.

This is only possible if it’s not too large. If you deal with particularly large data, please read the guide on iterating over datta batches (to come).

import lamindb as ln
import lnschema_bionty as lb
import anndata as ad

💡 loaded instance: testuser1/test-scrna (lamindb 0.55.2)

ln.track()

💡 notebook imports: anndata==0.9.2 lamindb==0.55.2 lnschema_bionty==0.31.2 scanpy==1.9.5

💡 Transform(id='mfWKm8OtAzp8z8', name='Analyze a dataset in memory', short_name='scrna4', version='0', type=notebook, updated_at=2023-10-10 15:43:51, created_by_id='DzTjkKse')

💡 Run(id='rBpXaKwLgV2rLNLLgYXP', run_at=2023-10-10 15:43:51, transform_id='mfWKm8OtAzp8z8', created_by_id='DzTjkKse')

ln.Dataset.filter().df()

	name	description	version	hash	reference	reference_type	transform_id	run_id	file_id	storage_id	initial_version_id	updated_at	created_by_id
id
oYS8NR45oBcEPgCISfCm	My versioned scRNA-seq dataset	None	1	6Hu1BywwK6bfIU2Dpku2xZ	None	None	Nv48yAceNSh8z8	RNgU2xx7TeUrL3d83b4F	oYS8NR45oBcEPgCISfCm	None	None	2023-10-10 15:42:41	DzTjkKse
oYS8NR45oBcEPgCISfHj	My versioned scRNA-seq dataset	None	2	JNjc88f22TLVPJHdgo7X	None	None	ManDYgmftZ8Cz8	JRscXJ0ZxufwqGUoGmIJ	None	None	oYS8NR45oBcEPgCISfCm	2023-10-10 15:43:32	DzTjkKse

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

dataset.files.df()

	storage_id	key	suffix	accessor	description	version	size	hash	hash_type	transform_id	run_id	initial_version_id	updated_at	created_by_id
id
oYS8NR45oBcEPgCISfCm	YpFBBtr4	None	.h5ad	AnnData	Conde22	None	57615999	6Hu1BywwK6bfIU2Dpku2xZ	sha1-fl	Nv48yAceNSh8z8	RNgU2xx7TeUrL3d83b4F	None	2023-10-10 15:42:41	DzTjkKse
wRXv3wXHrtOF3OihYYya	YpFBBtr4	None	.h5ad	AnnData	10x reference adata	None	857752	j6o6e27xPdqHQyT7Em_7MQ	md5	ManDYgmftZ8Cz8	JRscXJ0ZxufwqGUoGmIJ	None	2023-10-10 15:43:24	DzTjkKse

If the dataset doesn’t consist of too many files, we can now load it into memory.

Under-the-hood, the AnnData objects are concatenated during loading.

The amount of time this takes depends on a variety of factors.

If it occurs often, one might consider storing a concatenated version of the dataset, rather than the individual pieces.

adata = dataset.load()

The default is an outer join during concatenation as in pandas:

adata

AnnData object with n_obs × n_vars = 1718 × 36508
    obs: 'donor', 'tissue', 'cell_type', 'assay', 'n_genes', 'percent_mito', 'louvain', 'file_id'
    obsm: 'X_umap', 'X_pca'

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

adata.obs.file_id.cat.categories

Index(['oYS8NR45oBcEPgCISfCm', 'wRXv3wXHrtOF3OihYYya'], dtype='object')

We can easily obtain ensemble IDs for gene symbols using the look up object:

genes = lb.Gene.lookup(field="symbol")

genes.itm2b.ensembl_gene_id

'ENSG00000136156'

Let us create a plot:

import scanpy as sc

sc.pp.pca(adata, n_comps=2)

2023-10-10 15:43:56,153:INFO - Failed to extract font properties from /usr/share/fonts/truetype/noto/NotoColorEmoji.ttf: In FT2Font: Can not load face (unknown file format; error code 0x2)

2023-10-10 15:43:56,278:INFO - generated new fontManager

sc.pl.pca(
    adata,
    color=genes.itm2b.ensembl_gene_id,
    title=(
        f"{genes.itm2b.symbol} / {genes.itm2b.ensembl_gene_id} /"
        f" {genes.itm2b.description}"
    ),
    save="_itm2b",
)

WARNING: saving figure to file figures/pca_itm2b.pdf

file = ln.File("./figures/pca_itm2b.pdf", description="My result on ITM2B")
file.save()

file.view_flow()

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>