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analysis.umap

logger_config​

logger​

umap_embedding​

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

Perform UMAP embedding for given file and parameters.

Parameters

  • cfg (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) -> plt.Figure

Visualize UMAP embedding without labels.

Parameters

  • embed (np.ndarray): UMAP embedding.
  • num_points (int): Number of data points to visualize.

Returns

  • plt.Figure: Plot Visualization of UMAP embedding.

umap_label_vis​

def umap_label_vis(embed: np.ndarray, label: np.ndarray,
                   num_points: int) -> plt.Figure

Visualize UMAP embedding with motif labels.

Parameters

  • embed (np.ndarray): UMAP embedding.
  • label (np.ndarray): Motif labels.
  • num_points (int): Number of data points to visualize.

Returns

  • plt.Figure: Plot figure of UMAP visualization embedding with motif labels.

umap_vis_comm​

def umap_vis_comm(embed: np.ndarray, community_label: np.ndarray,
                  num_points: int) -> plt.Figure

Visualize UMAP embedding with community labels.

Parameters

  • embed (np.ndarray): UMAP embedding.
  • community_label (np.ndarray): Community labels.
  • num_points (int): Number of data points to visualize.

Returns

  • plt.Figure: Plot figure of UMAP visualization embedding with community labels.

visualize_umap​

@save_state(model=VisualizeUmapFunctionSchema)
def visualize_umap(config: dict,
                   segmentation_algorithm: SegmentationAlgorithms,
                   label: Optional[str] = None,
                   save_logs: bool = False) -> None

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

If label is None (UMAP visualization without labels):

  • 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.
  • segmentation_algorithm (SegmentationAlgorithms): Which segmentation algorithm to use. Options are 'hmm' or 'kmeans'.
  • label (str, optional): Type of labels to visualize. Options are None, 'motif' or 'community'. Default is None.
  • save_logs (bool, optional): Save logs to file. Default is False.

Returns

  • None