scirpy.tl.spectratype#
- scirpy.tl.spectratype(adata, chain='VJ_1', *, target_col, cdr3_col='junction_aa', combine_fun=<function sum>, fraction=None, airr_mod='airr', airr_key='airr', chain_idx_key='chain_indices', **kwargs)#
Summarizes the distribution of CDR3 region lengths.
Ignores NaN values.
- Parameters:
adata (
Union
[AnnData
,MuData
,DataHandler
]) – AnnData or MuData object that contains AIRR information.chain (
Union
[Literal
['VJ_1'
,'VJ_2'
,'VDJ_1'
,'VDJ_2'
],Sequence
[Literal
['VJ_1'
,'VJ_2'
,'VDJ_1'
,'VDJ_2'
]]] (default:'VJ_1'
)) – One or multiple chains from which to use CDR3 sequencestarget_col (
str
) – Color by this column fromobs
. E.g. sample or diagnosiscdr3_col (
str
(default:'junction_aa'
)) – AIRR rearrangement column from which sequences are obtainedcombine_fun (
Callable
(default:<function sum at 0x7f7c9d7d0eb0>
)) – A function definining how the groupby columns should be merged (e.g. sum, mean, median, etc).fraction (
Union
[str
,bool
,None
] (default:None
)) – If True, compute fractions of abundances relative to thegroupby
column rather than reporting abosolute numbers. Alternatively, a column name can be provided according to that the values will be normalized.airr_mod (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 (default:
'airr'
) – Key under which the AIRR information is stored in adata.obsm as an awkward array.chain_idx_key (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 DataFrame with spectratype information.