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visualization.umap

logger_config​

logger​

umap_embedding​

def umap_embedding(config: dict, num_points: int = 30_000) -> xr.Dataset

Perform UMAP embedding for a sample of the entire project.

Parameters

  • config (dict): Configuration parameters.
  • num_points (int): Number of points to use for UMAP embedding. Default is 30,000.

Returns

  • xr.Dataset: UMAP embedding and accompanying data for the sampled indices.

umap_vis_matplotlib​

def umap_vis_matplotlib(embed: np.ndarray,
                        num_points: int = 30_000,
                        labels: Optional[np.ndarray] = None,
                        title: Optional[str] = None,
                        show_legend: bool = True,
                        label_type: str = "none") -> Figure

Visualize UMAP embedding.

Parameters

  • embed (np.ndarray): UMAP embedding.
  • num_points (int): Number of data points to visualize. Default is 30,000.
  • labels (np.ndarray, optional): Motif or community labels. Default is None.
  • title (str, optional): Title for the plot. Default is None.
  • show_legend (bool, optional): Whether to show legend for labeled plots. Default is True.
  • label_type (str, optional): Type of labels ('none', 'motif', 'community'). Default is 'none'.

Returns

  • Figure: Matplotlib figure object.

umap_vis_plotly​

def umap_vis_plotly(embed: np.ndarray,
                    labels_motif: Optional[np.ndarray] = None,
                    labels_community: Optional[np.ndarray] = None,
                    session_names: Optional[list] = None,
                    num_points: int = 30_000,
                    title: str = "UMAP",
                    marker_size: float = 3.5,
                    marker_opacity: float = 0.7) -> go.Figure

Create an interactive Plotly UMAP scatter with dropdown to select labels:

  • None: grey points
  • Motif: colored by motif labels
  • Community: colored by community labels
  • Session: colored by session labels

Parameters

  • embed (np.ndarray): 2D UMAP embedding array of shape (N,2).
  • labels_motif (np.ndarray or None): 1D motif labels of length N.
  • labels_community (np.ndarray or None): 1D community labels of length N.
  • session_names (list or None): List of session names for each point.
  • num_points (int): Maximum number of points to show.
  • title (str): Title for the figure. Defaults to "UMAP".
  • marker_size (float): Size of the markers in the plot.
  • marker_opacity (float): Opacity of the markers in the plot.

Returns

  • plotly.graph_objs.Figure: The interactive Plotly figure.

visualize_umap​

def visualize_umap(config: dict,
                   num_points: int = 30_000,
                   save_to_file: bool = True,
                   show_figure: Literal["none", "matplotlib", "plotly",
                                        "all"] = "none",
                   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/
      • umap_embedding.nc
    • reports/
      • umap/
        • umap_<model>_<seg>-<n_clusters>.png (UMAP visualization without labels)
        • umap_<model>_<seg>-<n_clusters>_motif.png (UMAP visualization with motif labels)
        • umap_<model>_<seg>-<n_clusters>_community.png (UMAP visualization with community labels)
        • umap_<model>_<seg>-<n_clusters>_interactive.html (Interactive UMAP visualization)

Parameters

  • config (dict): Configuration parameters.
  • num_points (int, optional): Number of data points to visualize. Default is 30,000.
  • save_to_file (bool, optional): Save the figure to file. Default is True.
  • show_figure (Literal["none", "matplotlib", "plotly", "all"], optional): Show the figure. Default is "none".
  • "none": do not show
  • "matplotlib": show with matplotlib
  • "plotly": show with plotly
  • "all": show with both matplotlib and plotly
  • save_logs (bool, optional): Save logs. Default is True.

Returns

  • None