cassiopeia.pp.convert_alleletable_to_lineage_profile#
- cassiopeia.pp.convert_alleletable_to_lineage_profile(allele_table, cut_sites=None, collapse_duplicates=True)[source]#
Converts an AlleleTable to a lineage profile.
Takes in an allele table that summarizes the indels observed at individual cellBC-intBC pairs and produces a lineage profile, which essentially is a pivot table over the cellBC / intBCs. Conceptually, these lineage profiles are identical to character matrices, only the values in the matrix are the actual indel identities.
- Parameters:
- allele_table
AlleleTable.
- cut_sites
Optional[List[str]] (default:None) Columns in the AlleleTable to treat as cut sites. If None, we assume that the cut-sites are denoted by columns of the form “r{int}” (e.g. “r1”)
- collapse_duplicates
bool(default:True) Whether or not to collapse duplicate character states present for a single cellBC-intBC pair. This option has no effect if there are no allele conflicts. Defaults to True.
- Return type:
- Returns:
An NxM lineage profile.