plot_interactive_mapper_graph

gtda.mapper.visualization.plot_interactive_mapper_graph(pipeline, data, layout='kamada_kawai', layout_dim=2, color_variable=None, node_color_statistic=None, color_by_columns_dropdown=False, plotly_kwargs=None)[source]

Plotting function for interactive Mapper graphs.

Provides functionality to interactively update parameters from the cover and clustering steps defined in pipeline. Nodes are colored according to color_variable. By default, the hovertext displays a globally unique ID and the number of elements associated with a given node.

Parameters

  • pipeline (MapperPipeline object) – Mapper pipeline to act on to data.

  • data (array-like of shape (n_samples, n_features)) – Data used to generate the Mapper graph. Can be a pandas dataframe.

  • layout (None, str or callable, optional, default: 'kamada-kawai') – Layout algorithm for the graph. Can be any accepted value for the layout parameter in the layout method of igraph.Graph. 1

  • layout_dim (int, default: 2) – The number of dimensions for the layout. Can be 2 or 3.

  • color_variable (object or None, optional, default: None) –

    Specifies which quantity is to be used for node coloring.

    1. If a numpy ndarray or pandas dataframe, color_variable must have the same length as data and is interpreted as a quantity of interest according to which node of the Mapper graph is to be colored (see node_color_statistic).

    2. If None then equivalent to passing data.

    3. If an object implementing transform or fit_transform, e.g. a scikit-learn estimator or pipeline, it is applied to data to generate the quantity of interest.

    4. If an index or string, or list of indices / strings, equivalent to selecting a column or subset of columns from data.

  • node_color_statistic (None, callable, or ndarray of shape (n_nodes,) or (n_nodes, 1), optional, default: None) – Specifies how to determine the colors of each node. If a numpy array, it must have the same length as the number of nodes in the Mapper graph, and its values are used directly for node coloring, ignoring color_variable. Otherwise, it can be a callable object which is used to obtain a summary statistic, within each Mapper node, of the quantity specified by color_variable. The default value None is equivalent to passing numpy.mean.

  • color_by_columns_dropdown (bool, optional, default: False) – If True, a dropdown widget is generated which allows the user to color Mapper nodes according to any column in data.

  • plotly_kwargs (dict, optional, default: None) – Keyword arguments to configure the Plotly Figure.

Returns

  • box (ipywidgets.VBox object)

  • A box containing the following widgets (parameters of the clustering)

  • algorithm, parameters for the covering scheme, a Mapper graph arising

  • from those parameters, a validation box, and logs.

References

1

igraph.Graph.layout documentation.