scirpy.io.from_dandelion

scirpy.io.from_dandelion(dandelion, transfer=False, **kwargs)

Import data from Dandelion ([SRB+21]).

Internally calls scirpy.io.read_airr().

Note

Reading data into Scirpy has the following constraints:

  • Each cell can have up to four productive chains chains (Dual IR): two VJ and two VDJ chains.

  • Excess chains are ignored (those with lowest read count/UMI count) and cells flagged as Multichain-cell.

  • Non-productive chains are ignored.

  • Chain loci must be valid IMGT locus names.

  • Excess chains, non-productive chains, chains without a CDR3 sequence, or chains with invalid loci are serialized to JSON and stored in the extra_chains column. They are not used by scirpy except when exporting the AnnData object to AIRR format.

For more information, see Immune receptor (IR) model.

Parameters
dandelion

a dandelion.Dandelion instance

transfer : bool (default: False)

Whether to execute dandelion.tl.transfer to transfer all data to the anndata.AnnData instance.

**kwargs

Additional arguments passed to scirpy.io.read_airr().

Return type

AnnData

Returns

A AnnData instance with AIRR information stored in obs.