larry._tools._count_fate_values

Module Contents

Classes

FateValues

Helper class that provides a standard way to create an ABC using

Functions

count_t0_cell_fates(adata[, key_added, return_df])
d2_cell_fate_matrix(adata[, time_key, lineage_key])
count_fate_values(adata[, origin_time, fate_time, ...])	Count fate values.

class larry._tools._count_fate_values.FateValues(adata, origin_time=[2], fate_time=[4, 6], annotation_key='Cell type annotation', time_key='Time point', lineage_key='clone_idx')

Bases: larry._utils.AutoParseBase

Helper class that provides a standard way to create an ABC using inheritance.

_count_values_at_lineage_fate(df, labels_excluded=['undiff'])

df is the pandas.DataFrame obs table for a single clonal lineage

__call__() → pandas.DataFrame

Takes ~13s for the in vitro dataset

larry._tools._count_fate_values.count_t0_cell_fates(adata, key_added='cell_fate_df', return_df=False)

larry._tools._count_fate_values.d2_cell_fate_matrix(adata, time_key: str = 'Time point', lineage_key: str = 'clone_idx')

larry._tools._count_fate_values.count_fate_values(adata, origin_time=[2], fate_time=[4, 6], annotation_key='Cell type annotation', time_key='Time point', lineage_key='clone_idx', key_added='fate_counts', return_dfs=False)

Count fate values.