scirpy.io.AirrCell

class scirpy.io.AirrCell(cell_id, cell_attribute_fields=(), *, logger=<module 'scanpy.logging' from '/opt/hostedtoolcache/Python/3.8.10/x64/lib/python3.8/site-packages/scanpy/logging.py'>)

Data structure for a Cell with immune receptors. Represents one row of adata.obs.

This data structure is compliant with the AIRR rearrangement schema v1.0. An AirrCell can hold multiple chains (i.e. rows from the rearrangement TSV) which belong to the same cell. A chain is represented as a dictionary, where the keys are AIRR-rearrangement fields.

The AirrCell can, additionally, hold cell-level attributes which can be set in a dict-like fashion. Keys marked as “cell-level” via cell_attribute_fields will be automatically transferred to the cell-level when added through a chain. They are required to have the same value for all chains.

Parameters

cell_id : strstr

cell id or barcode. Needs to match the cell id used for transcriptomics data (i.e. the adata.obs_names)

cell_attribute_fields : Collection[str]Collection[str] (default: ())

List of field-names which are supposed to be stored at the cell-level rather than the chain level. If a chain with these fields is added to the cell, they are set on the cell-level instead. If the values already exist on the cell-level, a ValueError is raised, if they differ from the values that are already present.

logger

A logger to write messages to. If not specified, use scanpy’s default logger.

Attributes

VALID_LOCI	Valid chains are IMGT locus names see https://docs.airr-community.org/en/latest/datarep/rearrangements.html#locus-names
VDJ_LOCI	Identifiers of loci with a V-D-J junction
VJ_LOCI	Identifiers of loci with a V-J junction
cell_id	Unique identifier (barcode) of the cell.
chains	List of chain-dictionaries added to the cell.
fields	Return a list of all fields (chain-level and cell-level)

Methods

add_chain(chain)	Add a chain to the cell.
add_serialized_chains(serialized_chains)	Add chains serialized as JSON.
clear()
empty_chain_dict()	Generate an empty chain dictionary, containing all required AIRR columns, but set to None
get(k[,d])
items()
keys()
pop(k[,d])	If key is not found, d is returned if given, otherwise KeyError is raised.
popitem()	as a 2-tuple; but raise KeyError if D is empty.
setdefault(k[,d])
to_airr_records()	Iterate over chains as AIRR-Rearrangent compliant dictonaries.
to_scirpy_record([include_fields])	Convert the cell to a scirpy record (i.e.
update([E, ]**F)	If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v
values()