LaminR: Work with LaminDB instances in R

This package allows you to query and download data from LaminDB instances.

Setup

Install the development version from GitHub:

# install.packages("remotes")
remotes::install_github("laminlabs/laminr")

You will also need to install lamindb:

pip install lamindb[bionty,wetlab]

Connect to an instance

To connect to a LaminDB instance, you will first need to run lamin login OR lamin load <instance> in the terminal. This will create a directory in your home directory called .lamin with the necessary credentials.

lamin login
lamin connect laminlabs/cellxgene

Then, you can connect to the instance using the laminr::connect() function:

library(laminr)

db <- connect("laminlabs/cellxgene")
db

cellxgene Instance(modules='c('core', 'bionty')')

Query the instance

You can use the db object to query the instance:

artifact <- db$Artifact$get("KBW89Mf7IGcekja2hADu")

You can print the record:

artifact

Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, size=691757462, is_latest=TRUE, created_by_id=1, type='dataset', _hash_type='md5-n', n_observations=51552, created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', run_id=27, suffix='.h5ad', visibility=1, _key_is_virtual=FALSE, hash='SZ5tB0T4YKfiUuUkAL09ZA')

Or call the $describe() method to get a summary:

artifact$describe()

Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, size=691757462, is_latest=TRUE, created_by_id=1, type='dataset', _hash_type='md5-n', n_observations=51552, created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', run_id=27, suffix='.h5ad', visibility=1, _key_is_virtual=FALSE, hash='SZ5tB0T4YKfiUuUkAL09ZA')
  Provenance
    $storage = 's3://cellxgene-data-public'
    $transform = 'Census release 2024-07-01 (LTS)'
    $run = '2024-07-16T12:49:41.81955+00:00'
    $created_by = 'sunnyosun'

Access fields

You can access its fields as follows:

• artifact$id: 3659
• artifact$uid: KBW89Mf7IGcekja2hADu
• artifact$key: cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad

You can also fetch related fields:

• artifact$root: s3://cellxgene-data-public
• artifact$created_by: sunnyosun

Load the artifact

You can directly load the artifact to access its data:

artifact$load()

ℹ 's3://cellxgene-data-public/cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad' already exists at '/home/rcannood/.cache/lamindb/cellxgene-data-public/cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad'

AnnData object with n_obs × n_vars = 51552 × 36398
    obs: 'donor_id', 'Predicted_labels_CellTypist', 'Majority_voting_CellTypist', 'Manually_curated_celltype', 'assay_ontology_term_id', 'cell_type_ontology_term_id', 'development_stage_ontology_term_id', 'disease_ontology_term_id', 'self_reported_ethnicity_ontology_term_id', 'is_primary_data', 'organism_ontology_term_id', 'sex_ontology_term_id', 'tissue_ontology_term_id', 'suspension_type', 'tissue_type', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage', 'observation_joinid'
    var: 'gene_symbols', 'feature_is_filtered', 'feature_name', 'feature_reference', 'feature_biotype', 'feature_length'
    uns: 'cell_type_ontology_term_id_colors', 'citation', 'default_embedding', 'schema_reference', 'schema_version', 'sex_ontology_term_id_colors', 'title'
    obsm: 'X_umap'