CellScope.ts.visualize_tree_structured

CellScope.ts. visualize_tree_structured (Y_initial, label_step0, Y_1, Title_1, Y_all, Title_all, index_1, index_all, step0, step1, T, save_fig = False, save_path = ‘’)

The visualize_tree_structured function creates a series of UMAP-based scatter plots representing hierarchical clustering across different levels. It visually captures initial clusters, subclusters, and refined clusters, supporting tree-structured analysis of cell data. Optionally, it saves the figures to a specified directory.

Parameters

• Y_initial (np.ndarray):

  Initial 2D UMAP embedding of all cells.

• label_step0 (np.ndarray):

  Clustering labels at the starting level (step0).

• Y_1 (list of np.ndarray):

  List of UMAP embeddings for clusters at the first level.

• Title_1 (list):

  List of titles for the first-level clusters.

• Y_all (list of np.ndarray):

  List of UMAP embeddings for clusters at all levels.

• Title_all (list):

  List of titles for clusters at all levels.

• index_1 (list):

  List of indices corresponding to cells in each cluster at the first level.

• index_all (list):

  List of indices corresponding to cells in each cluster at all levels.

• step0 (int):

  Final starting level for the tree-structured visualization.

• step1 (int):

  Final ending level for the tree-structured visualization.

• T (np.ndarray):

  Matrix of clustering labels for different levels of clustering.

• save_fig (bool, optional, default=False):

  If True, saves the figures to the specified path.

• save_path (str, optional, default=’’):

  Directory path to save the figures. Required if save_fig=True.

Return

• This function does not return any values. It displays a grid of scatter plots showing UMAP embeddings for different clusters at different levels.