cassiopeia.pp.convert_alleletable_to_lineage_profile

cassiopeia.pp.convert_alleletable_to_lineage_profile(allele_table, cut_sites=None, collapse_duplicates=True)

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 : List[str], NoneOptional[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 : boolbool (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

DataFrameDataFrame

Returns

An NxM lineage profile.