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visualization.umap

logger_config​

logger​

umap_embedding​

def umap_embedding(
        config: dict, session: str, model_name: str, n_clusters: int,
        segmentation_algorithm: SegmentationAlgorithms) -> np.ndarray

Perform UMAP embedding for given file and parameters.

Parameters

  • config (dict): Configuration parameters.
  • session (str): Session name.
  • model_name (str): Model name.
  • n_clusters (int): Number of clusters.
  • segmentation_algorithm (str): Segmentation algorithm.

Returns

  • np.ndarray: UMAP embedding.

umap_vis​

def umap_vis(embed: np.ndarray,
             num_points: int,
             labels: Optional[np.ndarray] = None,
             save_to_file: bool = False,
             show_figure: bool = True) -> Figure

Visualize UMAP embedding.

Parameters

  • embed (np.ndarray): UMAP embedding.
  • num_points (int): Number of data points to visualize.
  • labels (np.ndarray, optional): Motif or community labels. Default is None.

Returns

  • Figure: Matplotlib figure object.

visualize_umap​

def visualize_umap(config: dict,
                   save_to_file: bool = True,
                   show_figure: bool = True,
                   save_logs: bool = True) -> None

Visualize UMAP embeddings based on configuration settings. Fills in the values in the "visualization_umap" key of the states.json file. Saves results files at:

  • project_name/
    • results/
      • file_name/
        • model_name/
          • segmentation_algorithm-n_clusters/
            • community/
              • umap_embedding_file_name.npy
              • umap_vis_label_none_file_name.png (UMAP visualization without labels)
              • umap_vis_motif_file_name.png (UMAP visualization with motif labels)
              • umap_vis_community_file_name.png (UMAP visualization with community labels)

Parameters

  • config (dict): Configuration parameters.
  • save_to_file (bool, optional): Save the figure to file. Default is True.
  • show_figure (bool, optional): Show the figure. Default is True.
  • save_logs (bool, optional): Save logs. Default is True.

Returns

  • None