CellScope.ga.Gene_Analysis

CellScope.ga. Gene_Analysis (fea : np.ndarray, layer : list | np.ndarray)

The Gene_Analysis function calculates Wasserstein distances [PZ19] between gene expressions in different clusters defined by layer, classifying genes as Housekeeper Gene, Type-Related Gene, or Type-Determining Gene based on their roles across layers.

Parameters

• fea (np.ndarray):

  The feature matrix of shape (n_cell, n_gene), where rows correspond to cells and columns to genes.

• layer (list | np.ndarray):

  List or array indicating clusters. Must contain an even number of elements representing paired clusters for comparison.

Return

• Res (np.ndarray):

  Wasserstein distances of shape (num_Gene, len_flow), where len_flow is half the length of layer.

• label (np.ndarray):

  Integer matrix indicating gene categories for each flow, with values: 0 (‘Housekeeper Gene’), 1 (‘Type-Related Gene’), or 2 (‘Type-Determining Gene’).

• label_str (np.ndarray):

  String matrix with the same shape as label, containing gene type labels.

• flow_labels (np.ndarray):

  Array indicating flow labels for genes based on their category across layers.