dandelion.utilities.from_scirpy

dandelion.utilities.from_scirpy(adata, clone_key=None, key_added=None, mapping_mode='chain')[source]

Reads a scirpy initialized AnnData oject and returns a Dandelion object.

Parameters
  • adata (AnnData) – scirpy initialized AnnData object.

  • clone_key (str, optional) – column name for clone_id in AnnData. None defaults to clonotype in scirpy initialized object.

  • key_added (str, optional) – column name for clone_id in Dandelion. None defaults to clone_id in dandelion initialized object.

  • mapping_mode (str) – mode for retrieving the clone_id calls, either based on cells (all chains/contigs have the same call) or chains (allow for different calls between chains).

Returns

Return type

Dandelion object.