GroupByGenotype

missionbio.mosaic.algorithms.group_by_genotype.GroupByGenotype

class GroupByGenotype(dna: Dna, features, layer='NGT', group_missing=True, max_ado_score=0.8, min_clone_size=1, ignore_zygosity=False)

See group_by_genotype() for the complete documentation

Functions

get_labels()	Group the cells based on genotype using the given parameters.
get_ado_scores()	ADO score for each clone.
subclone_table()	per-clone statistics
plot([kind])	Plots the data used to derive the ADO score

Parameters:

dnaDna

The Dna assay object

featureslist-like

The features which are to be considered while allocating the groups formed by the genotype.

layerstr

Name of the layer used to count the cell types. Expected values are NGT or NGT_FILTERED as obtained from the filter_variants() method.

group_missingbool

Whether the clusters caused due to missing values are merged together under one cluster named ‘Missing’.

max_ado_scorefloat [0, 1]

The maximum ADO score of a clone before it is grouped into the “ADO” clone category.

min_clone_sizefloat [0, 100]

The minimumum proportion of total cells to be present in the clone to count it as a separate clone.

ignore_zygositybool

Whether HET and HOM are considered the same or not