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Persistence graphical tools user manual
=======================================
Definition
----------
.. include:: persistence_graphical_tools_sum.inc


Show persistence as a barcode
-----------------------------

This function can display the persistence result as a barcode:

.. plot::
   :include-source:

    import gudhi

    perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt'
    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file)
    diag = periodic_cc.persistence()
    print("diag = ", diag)
    plt = gudhi.plot_persistence_barcode(diag)
    plt.show()

Show persistence as a diagram
-----------------------------

This function can display the persistence result as a diagram:

.. plot::
   :include-source:

    import gudhi

    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
    persistence_file=gudhi.__root_source_dir__ + \
        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
    plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file,
        legend=True)
    plt.show()

If you want more information on a specific dimension, for instance:

.. plot::
   :include-source:

    import gudhi

    persistence_file=gudhi.__root_source_dir__ + \
        '/data/persistence_diagram/rips_on_tore3D_1307.pers'
    diag = \
        gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\
            persistence_file)
    dim = 1
    # Display all points with some transparency
    plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]],
        max_plots=0, alpha=0.1)
    plt.show()