cospar.pp.refine_state_info_by_leiden_clustering

cospar.pp.refine_state_info_by_leiden_clustering(adata, selected_key='state_info', selected_values=None, resolution=0.5, n_neighbors=20, confirm_change=False, cluster_name_prefix='S')

Refine state info by clustering states at given time points.

Select states at desired time points to improve the clustering. When first run, set confirm_change=False. Only when you are happy with the result, set confirm_change=True to update adata.obs[‘state_info’]. The original state_info will be stored at adata.obs[‘old_state_info’].

Parameters

adata : AnnData object

selected_key

A key in adata.obs, including ‘state_info’, or ‘time_info’

selected_values : list, optional (default: include all)

A list of clusters/time_points for further sub-clustering. Should be among adata.obs[selected_key].

adata

n_neighbors : int, optional (default: 20)

Neighber number for constructing the KNN graph, using the UMAP method.

resolution : float, optional (default: 0.5)

A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters.

confirm_change : bool, optional (default: False)

If True, update adata.obs[‘state_info’]

cluster_name_prefix : str, optional (default: ‘S’)

prefix for the new cluster name to distinguish it from existing cluster names.

Returns

Update adata.obs[‘state_info’] if confirm_change=True.