cassiopeia.pp.convert_lineage_profile_to_character_matrix#
- cassiopeia.pp.convert_lineage_profile_to_character_matrix(lineage_profile, indel_priors=None, missing_allele_indicator=None, missing_state_indicator=-1)[source]#
Converts a lineage profile to a character matrix.
Takes in a lineage profile summarizing the explicit indel identities observed at each cut site in a cell and converts this into a character matrix where the indels are abstracted into integers.
Note
The lineage profile is converted directly into a character matrix, without performing any collapsing of duplicate states. Instead, this should have been done in the previous step, when calling
convert_alleletable_to_lineage_profile().- Parameters:
- lineage_profile
DataFrame Lineage profile
- indel_priors
DataFrame|NoneOptional[DataFrame] (default:None) Dataframe mapping indels to prior probabilities
- missing_allele_indicator
str|NoneOptional[str] (default:None) An allele that is being used to represent missing data.
- missing_state_indicator
int(default:-1) State to indicate missing data
- lineage_profile
- Return type:
Tuple[DataFrame,Dict[int,Dict[int,float]],Dict[int,Dict[int,str]]]- Returns:
- A character matrix, prior probability dictionary, and mapping from
character/state pairs to indel identities.