scirpy.io.from_airr_cells

scirpy.io.from_airr_cells#

scirpy.io.from_airr_cells(airr_cells, key_added='airr')#

Convert a collection of AirrCell objects to AnnData.

This is useful for converting arbitrary data formats into the scirpy Storing AIRR rearrangement data in AnnData.

Even though data without these fields can be imported, the following columns are required by scirpy for a meaningful analysis:

  • cell_id

  • productive

  • locus containing a valid IMGT locus name

  • at least one of consensus_count, duplicate_count, or umi_count

  • at least one of junction_aa or junction.

Note

Since scirpy v0.13, there are no restrictions on the AIRR data that can be stored in the scirpy data structure, except that each receptor chain needs to be associated with a cell.

The scirpy Immune receptor (IR) model is now applied in later step using the index_chains() function.

For more information, see Storing AIRR rearrangement data in AnnData.

Parameters:

airr_cells (Iterable[AirrCell]) – A list of AirrCell objects

Return type:

AnnData

Returns:

AnnData object with IR information in obs.