scirpy.get.airr#
- scirpy.get.airr(adata, airr_variable, chain=('VJ_1', 'VDJ_1', 'VJ_2', 'VDJ_2'), *, airr_mod='airr', airr_key='airr', chain_idx_key='chain_indices')#
Retrieve AIRR variables for each cell, given a specific chain.
- Parameters:
adata (
Union
[AnnData
,MuData
,DataHandler
]) – AnnData or MuData object that contains AIRR information.airr_variable (
str
|Sequence
[str
]) – One or multiple columns from the AIRR Rearrangment schema (see adata.var). If multiple values are specified, a dataframe will be returned.chain (
Union
[Literal
['VJ_1'
,'VJ_2'
,'VDJ_1'
,'VDJ_2'
],Sequence
[Literal
['VJ_1'
,'VJ_2'
,'VDJ_1'
,'VDJ_2'
]]] (default:('VJ_1', 'VDJ_1', 'VJ_2', 'VDJ_2')
)) – choose the recptor arm (VJ/VDJ) and if you want to retrieve the primary or secondary chain. If multiple chains are specified, a adataframe will be returnedairr_mod (
str
(default:'airr'
)) – Name of the modality with AIRR information is stored in theMuData
object. if anAnnData
object is passed to the function, this parameter is ignored.airr_key (
str
(default:'airr'
)) – Key under which the AIRR information is stored in adata.obsm as an awkward array.chain_idx_key (
str
(default:'chain_indices'
)) – Key under which the chain indices are stored in adata.obsm. If chain indices are not present,index_chains()
is run with default parameters.
- Return type:
- Returns:
A
Series
orDataFrame
aligned toadata.obs
. Contains missing values in places where a cell does not have the requested chain.