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
]Union
[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 : {‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’} |
Sequence
[Literal
[‘VJ_1’, ‘VJ_2’, ‘VDJ_1’, ‘VDJ_2’]]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 returned
- airr_mod :
str
(default:'airr'
) Name of the modality with AIRR information is stored in the
MuData
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.