shnitsel.vis.plot.kde
=====================

.. py:module:: shnitsel.vis.plot.kde


Functions
---------

.. autoapisummary::

   shnitsel.vis.plot.kde.fit_kdes
   shnitsel.vis.plot.kde.eval_kdes
   shnitsel.vis.plot.kde.get_xx_yy
   shnitsel.vis.plot.kde.fit_and_eval_kdes
   shnitsel.vis.plot.kde.plot_kdes
   shnitsel.vis.plot.kde.biplot_kde
   shnitsel.vis.plot.kde.plot_cdf_for_kde


Module Contents
---------------

.. py:function:: fit_kdes(noodle, geo_prop, geo_filter)

.. py:function:: eval_kdes(kernels, xx, yy)

.. py:function:: get_xx_yy(noodle, fineness=500, extension=0.1)

.. py:function:: fit_and_eval_kdes(noodle, geo_prop, geo_filter, fineness=500, extension=0.1)

.. py:function:: plot_kdes(xx, yy, Zs, colors=None, levels=None, fill=True, fig=None, ax=None)

.. py:function:: biplot_kde(frames, at1 = 0, at2 = 1, at3 = None, at4 = None, geo_filter = None, levels = None, scatter_color = 'time', fill = True, nbins=4, mean=False)

   Generates a biplot that visualizes PCA projections and kernel density estimates (KDE)
   of a property (distance, angle, dihedral angle) describing the geometry of specified
   atoms. The property is chosen based on the number of atoms specified:

   * 2 atoms => distance
   * 3 atoms => angle
   * 4 atoms => dihedral angle

   :param frames: A dataset containing trajectory frames with atomic coordinates.
   :param at1: Indices of the first, second, third and fourth atoms for geometric property calculation.
   :param at2: Indices of the first, second, third and fourth atoms for geometric property calculation.
   :param at3: Indices of the first, second, third and fourth atoms for geometric property calculation.
   :param at4: Indices of the first, second, third and fourth atoms for geometric property calculation.
   :param geo_filter: A list of tuples representing ranges. A KDE is plotted for each range, indicating the distribution of
                      points for which the value of the geometry feature falls in that range.
   :param levels: Contour levels for the KDE plot. Defaults to [0.08, 1]. This parameter is passed to
                  matplotlib.axes.Axes.contour.
   :param scatter_color: Must be one of 'time' or 'geo'. If 'time', the scatter-points will be colored based on the time coordinate;
                         if 'geo', the scatter-points will be colored based on the relevant geometry feature (see above).
   :param fill: Whether to plot filled contours (``fill=True``, uses ``ax.contourf``)
                or just contour lines (``fill=False``, uses ``ax.contour``).
   :param nbins: number of bins to be visualized, must be an integer between 1 and 4

   :returns: The computed KDE data for the atom-atom distance distribution.
   :rtype: kde_dat

   .. rubric:: Notes

   * Computes a geometric property of the specified atoms across all frames.
   * Uses kernel density estimation (KDE) to analyze the distance distributions.
   * Performs PCA on trajectory pairwise distances and visualizes clustering of structural changes.
   * Produces a figure with PCA projection, cluster analysis, and KDE plots.


.. py:function:: plot_cdf_for_kde(z, level, ax=None)