Plotting utilities

class pyballmapper.plotting.graph_GUI(graph, my_palette, tooltips_variables=[], figsize=(800, 600), output_format='svg', render_seed=42, render_iterations=100, MIN_SIZE=7, MAX_SIZE=20)

Bases: object

Create a Bokeh plot rapresenting the BallMapper graph.

Parameters:

  • graph (NetworkX graph) – The Graph attribute of a BallMapper object.

  • my_palette (matplotlib palette) – The color palette used to color the nodes.

  • tooltips_variables (list of strings, default=None) – Which variables to show in the mouse hovertool.

  • figsize (tuple, default=(800, 600)) – The figure size.

  • output_format (string, default='svg') – The format in which the save button saves the plot.

  • render_seed (int, default=42) – Seed for the networkx spring_layout.

  • render_iterations (int, default=100) – Number of iterations for the networkx spring_layout.

  • MIN_SIZE (int, default=7) – Minimal size of the graph nodes.

  • int (MAX_SIZE;) – Maximal size of the graph nodes.

  • default=20 – Maximal size of the graph nodes.

Graph

The BallMapper graph. Each node correspond to a covering ball and has attributes: ‘landmark’ the id of the corresponding landmark point ‘points covered’ the ids of the points covered by the corresponding ball

Type:

NetworkX Graph object

eps

The input radius of the balls.

Type:

float

points_covered_by_landmarks

keys: landmarks ids values: list of ids of the points covered by the corresponding ball

Type:

dict

add_colorbar(num_ticks, low, high)

Add a colorbar to the right side of the Bokeh plot.

Parameters:

  • num_ticks (int) – Number of ticks, use a high number (100) for a continuos looking colorbar.

  • low (float) – Value at the bottom of the colorbar.

  • high (float) – Value at the top of the colorbar.

color_by_variable(variable, MIN_VALUE=inf, MAX_VALUE=-inf, logscale=False)

Color the BallMapper Bokeh plot nodes using a specific variable.

Coloring data can be added using the BallMapper.add_coloring() method. MIN_VALUE and MAX_VALUE are computed automatically, but lower (resp. higher) values can be manually specified.

Parameters:

  • variable (string) – Which coloring variable to use.

  • MIN_VALUE (float, default=np.inf) – Minimum value for the coloring palette.

  • MAX_VALUE (float, default=-np.inf) – Maximum value for the coloring palette.

  • logscale (bool, default=False) – Wheter to use a logscale coloring. If False, linear is used.

color_edges()

color edges by interpolating between the nodes’ colors

pyballmapper.plotting.kmapper_visualize(bm, coloring_df, path_html='output.html', title=None, **kwargs)

leverages kepler-mapper visualization tool to produce an interactive html. https://kepler-mapper.scikit-tda.org

Parameters:

  • bm (BallMapper) – the BallMapper graph to plot

  • coloring_df (pandas.DataFrame) – pandas dataframe of shape (n_samples, n_coloring_function)

  • path_html (str, optional) – the output file, by default ‘output.html’

  • title (string, optional) – title to be displayed in the top bar, by default None