CellScope.ts.tree_structure_visualization_step

CellScope.ts. tree_structure_visualization_step (T, step0, step1, Title_1, Title_all, Y_initial, Y_1, Y_all, index_1, index_all, **main_radius**=2.0, **orbit_radius**=1.5, **orbit_distance**=4.0, **branch_params**=None, **save_fig**=False, **save_path**=’’)

The tree_structure_visualization_step function progressively constructs the main trunk and branch components of the tree-structured visualization, enabling users to freely assemble them.

Parameters

  • T (np.ndarray):

    Matrix of clustering labels for different levels of clustering.

  • step0 (int):

    Final starting level for the tree-structured visualization.

  • step1 (int):

    Final ending level for the tree-structured visualization.

  • Title_1 (list):

    List of titles for the first-level clusters.

  • Title_all (list):

    List of titles for clusters at all levels.

  • Y_initial (np.ndarray):

    Initial 2D UMAP embedding of all cells.

  • Y_1 (list of np.ndarray):

    List of UMAP embeddings for clusters at the first level.

  • Y_all (list of np.ndarray):

    List of UMAP embeddings 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.

  • main_radius (float, optional, default=2.0):

    The node radius of the zeroth-layer nodes.

  • orbit_radius (float, optional, default=1.5):

    The node radius of the first-layer nodes.

  • orbit_distance (float, optional, default=4.0):

    The distance between the centers of the first-layer nodes and the zeroth-layer nodes.

  • branch_params (None or dict, optional, default=None):

    Additional parameters for branch customization.

  • 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_figure=True.

Returns

  • Two dictionaries R_dict and C_dict, containing node radii and center coordinates for plotting.