CellScope.gev.plot_clustered_heatmap

CellScope.gev. plot_clustered_heatmap (fea : np.ndarray, marker_gene_indices : list, marker_gene_name : list, cell_type : np.ndarray, save_fig : bool = False, save_path : str = None)

The plot_clustered_heatmap function generates a clustered heatmap that visualizes gene expression patterns across different cell types. It organizes cells based on their labels and marker gene expression, offering insights into gene expression clusters. The function also includes an option to save the heatmap as a file.

Parameters

• fea (np.ndarray | csr_matrix):

  Feature matrix for gene expression.

• marker_gene_indices (list):

  List of indices for marker genes.

• marker_gene_name (list):

  List of marker gene names.

• cell_type (np.ndarray):

  Array of cell type labels.

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

  If set to True, saves the figure to the specified path.

• save_path (str, optional):

  File path to save the figure. Required if save_fig=True.

Return

• This function does not return any values. It displays a clustered heatmap of gene expression.