dandelion.Dandelion

class dandelion.Dandelion(data=None, metadata=None, germline=None, layout=None, graph=None, initialize=True, library_type=None, **kwargs)[source]

Dandelion class object.

__init__(data=None, metadata=None, germline=None, layout=None, graph=None, initialize=True, library_type=None, **kwargs)[source]

Init method for Dandelion.

Parameters:

  • data (pd.DataFrame | Path | str | None, optional) – AIRR formatted data.

  • metadata (pd.DataFrame | None, optional) – AIRR data collapsed per cell.

  • germline (dict[str, str] | None, optional) – dictionary of germline gene:sequence records.

  • layout (tuple[dict[str, np.array], dict[str, np.array]] | None, optional) – node positions for computed graph.

  • graph (tuple[nx.Graph, nx.Graph] | None, optional) – networkx graphs for clonotype networks.

  • initialize (bool, optional) – whether or not to initialize .metadata slot.

  • library_type (Literal[“tr-ab”, “tr-gd”, “ig”] | None, optional) – One of “tr-ab”, “tr-gd”, “ig”.

  • **kwargs – passed to Dandelion.update_metadata.

Methods

__init__([data, metadata, germline, layout, ...])

Init method for Dandelion.

add_cell_prefix(prefix[, sync, ...])

Add prefix to cell_id and optionally to sequence_id.

add_cell_suffix(suffix[, sync, ...])

Add prefix to cell_id and optionally to sequence_id.

add_sequence_prefix(prefix[, sync, ...])

Add prefix to sequence_id and then apply to cell_id as well.

add_sequence_suffix(suffix[, sync, ...])

Add suffix to sequence_id and then apply to cell_id as well.

copy()

Performs a deep copy of all slots in Dandelion class.

reset_ids()

Reset both IDs to their original values.

simplify(**kwargs)

Disambiguate VDJ and C gene calls when there's multiple calls separated by commas and strip the alleles.

store_germline_reference([corrected, ...])

Update germline reference with corrected sequences and store in Dandelion object.

update_metadata([retrieve, clone_key, ...])

A Dandelion initialisation function to update and populate the .metadata slot.

update_plus([option])

Retrieve additional data columns that are useful.

write([filename, compression, ...])

Writes a Dandelion class to .h5ddl format.

write_10x([folder, filename_prefix, ...])

Writes a Dandelion class to 10x formatted files so that it can be ingested for other tools.

write_airr([filename])

Writes a Dandelion class to AIRR formatted .tsv format.

write_h5ddl([filename, compression, ...])

Writes a Dandelion class to .h5ddl format.

write_pkl([filename])

Writes a Dandelion class to .pkl format.

Attributes

data

One-dimensional annotation of contig observations (pd.DataFrame).

data_names

Names of observations (alias for .data.index).

metadata

One-dimensional annotation of cell observations (pd.DataFrame).

metadata_names

Names of observations (alias for .metadata.index).