larry._tools._annotate_fated

Module Contents

Functions

fated_idx(, lineage_key, time_key)

generate a list of lineages that are seen at d2 as well as d4 and d6

annotate_fated() → None)

We use this function to denote lineages with cells at d2
larry._tools._annotate_fated.fated_idx(adata, fate_time=[4, 6], exclude_fate: tuple = ('Cell type annotation', ['undiff']), lineage_key: str = 'clone_idx', time_key: str = 'Time point') → list

generate a list of lineages that are seen at d2 as well as d4 and d6

  1. This function returns the indices of lineages NOT cells.

larry._tools._annotate_fated.annotate_fated(adata, lineage_key='clone_idx', time_key='Time point', t0=2, fate_time=[4, 6], key_added='fate_observed', t0_key_added='t0_fated', exclude_fate: tuple = ('Cell type annotation', ['undiff'])) → None

We use this function to denote lineages with cells at d2 and one or more cells in [d4, d6]

Updates adata.obs with two columns -> adata.obs[[‘fate_observed’, ‘t0_fated’]]