scirpy.get.airr_context#
- scirpy.get.airr_context(data, airr_variable, chain=('VJ_1', 'VDJ_1', 'VJ_2', 'VDJ_2'), *, airr_mod='airr', airr_key='airr', chain_idx_key='chain_indices')#
Contextmanager that temporarily adds AIRR information to obs.
This is essentially a wrapper around
obs_context()
and equivalent toir.get.obs_context(data, ir.get.airr(airr_variable, chain))
Example
To list all combinations of patient and V genes in the VJ and VDJ chains:
with ir.get.airr_context(mdata, "v_call", chain=["VJ_1", "VDJ_1"]) as m: combinations = ( m.obs.groupby(["patient", "VJ_1_v_call", "VDJ_1_v_call"], observed=True) .size() .reset_index(name="n") )
- Parameters:
adata – 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.