pymatgen.util.plotting — pymatgen 2020.7.3 documentation

# Source code for pymatgen.util.plotting

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.
    """
    Utilities for generating nicer plots.
    """
    import math
    import numpy as np

    from pymatgen.core.periodic_table import Element

    __author__ = "Shyue Ping Ong"
    __copyright__ = "Copyright 2012, The Materials Project"
    __version__ = "0.1"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __date__ = "Mar 13, 2012"

    def pretty_plot(width=8, height=None, plt=None, dpi=None,
                    color_cycle=("qualitative", "Set1_9")):
        """
        Provides a publication quality plot, with nice defaults for font sizes etc.

        Args:
            width (float): Width of plot in inches. Defaults to 8in.
            height (float): Height of plot in inches. Defaults to width * golden
                ratio.
            plt (matplotlib.pyplot): If plt is supplied, changes will be made to an
                existing plot. Otherwise, a new plot will be created.
            dpi (int): Sets dot per inch for figure. Defaults to 300.
            color_cycle (tuple): Set the color cycle for new plots to one of the
                color sets in palettable. Defaults to a qualitative Set1_9.

        Returns:
            Matplotlib plot object with properly sized fonts.
        """
        ticksize = int(width * 2.5)

        golden_ratio = (math.sqrt(5) - 1) / 2

        if not height:
            height = int(width * golden_ratio)

        if plt is None:
            import matplotlib.pyplot as plt
            import importlib
            mod = importlib.import_module("palettable.colorbrewer.%s" %
                                          color_cycle[0])
            colors = getattr(mod, color_cycle[1]).mpl_colors
            from cycler import cycler

            plt.figure(figsize=(width, height), facecolor="w", dpi=dpi)
            ax = plt.gca()
            ax.set_prop_cycle(cycler('color', colors))
        else:
            fig = plt.gcf()
            fig.set_size_inches(width, height)
        plt.xticks(fontsize=ticksize)
        plt.yticks(fontsize=ticksize)

        ax = plt.gca()
        ax.set_title(ax.get_title(), size=width * 4)

        labelsize = int(width * 3)

        ax.set_xlabel(ax.get_xlabel(), size=labelsize)
        ax.set_ylabel(ax.get_ylabel(), size=labelsize)

        return plt

    def pretty_plot_two_axis(x, y1, y2, xlabel=None, y1label=None, y2label=None,
                             width=8, height=None, dpi=300, **plot_kwargs):
        """
        Variant of pretty_plot that does a dual axis plot. Adapted from matplotlib
        examples. Makes it easier to create plots with different axes.

        Args:
            x (np.ndarray/list): Data for x-axis.
            y1 (dict/np.ndarray/list): Data for y1 axis (left). If a dict, it will
                be interpreted as a {label: sequence}.
            y2 (dict/np.ndarray/list): Data for y2 axis (right). If a dict, it will
                be interpreted as a {label: sequence}.
            xlabel (str): If not None, this will be the label for the x-axis.
            y1label (str): If not None, this will be the label for the y1-axis.
            y2label (str): If not None, this will be the label for the y2-axis.
            width (float): Width of plot in inches. Defaults to 8in.
            height (float): Height of plot in inches. Defaults to width * golden
                ratio.
            dpi (int): Sets dot per inch for figure. Defaults to 300.
            plot_kwargs: Passthrough kwargs to matplotlib's plot method. E.g.,
                linewidth, etc.

        Returns:
            matplotlib.pyplot
        """

        import palettable.colorbrewer.diverging

        colors = palettable.colorbrewer.diverging.RdYlBu_4.mpl_colors
        c1 = colors[0]
        c2 = colors[-1]

        golden_ratio = (math.sqrt(5) - 1) / 2

        if not height:
            height = int(width * golden_ratio)

        import matplotlib.pyplot as plt
        width = 12
        labelsize = int(width * 3)
        ticksize = int(width * 2.5)
        styles = ["-", "--", "-.", "."]

        fig, ax1 = plt.subplots()
        fig.set_size_inches((width, height))
        if dpi:
            fig.set_dpi(dpi)
        if isinstance(y1, dict):
            for i, (k, v) in enumerate(y1.items()):
                ax1.plot(x, v, c=c1, marker='s', ls=styles[i % len(styles)],
                         label=k, **plot_kwargs)
            ax1.legend(fontsize=labelsize)
        else:
            ax1.plot(x, y1, c=c1, marker='s', ls='-', **plot_kwargs)

        if xlabel:
            ax1.set_xlabel(xlabel, fontsize=labelsize)

        if y1label:
            # Make the y-axis label, ticks and tick labels match the line color.
            ax1.set_ylabel(y1label, color=c1, fontsize=labelsize)

        ax1.tick_params('x', labelsize=ticksize)
        ax1.tick_params('y', colors=c1, labelsize=ticksize)

        ax2 = ax1.twinx()
        if isinstance(y2, dict):
            for i, (k, v) in enumerate(y2.items()):
                ax2.plot(x, v, c=c2, marker='o', ls=styles[i % len(styles)],
                         label=k)
            ax2.legend(fontsize=labelsize)
        else:
            ax2.plot(x, y2, c=c2, marker='o', ls='-')

        if y2label:
            # Make the y-axis label, ticks and tick labels match the line color.
            ax2.set_ylabel(y2label, color=c2, fontsize=labelsize)

        ax2.tick_params('y', colors=c2, labelsize=ticksize)
        return plt

    def pretty_polyfit_plot(x, y, deg=1, xlabel=None, ylabel=None, **kwargs):
        r"""
        Convenience method to plot data with trend lines based on polynomial fit.

        Args:
            x: Sequence of x data.
            y: Sequence of y data.
            deg (int): Degree of polynomial. Defaults to 1.
            xlabel (str): Label for x-axis.
            ylabel (str): Label for y-axis.
            \\*\\*kwargs: Keyword args passed to pretty_plot.

        Returns:
            matplotlib.pyplot object.
        """
        plt = pretty_plot(**kwargs)
        pp = np.polyfit(x, y, deg)
        xp = np.linspace(min(x), max(x), 200)
        plt.plot(xp, np.polyval(pp, xp), 'k--', x, y, 'o')
        if xlabel:
            plt.xlabel(xlabel)
        if ylabel:
            plt.ylabel(ylabel)
        return plt

    def periodic_table_heatmap(elemental_data, cbar_label="", cbar_label_size=14,
                               show_plot=False, cmap="YlOrRd", cmap_range=None, blank_color="grey",
                               value_format=None, max_row=9):
        """
        A static method that generates a heat map overlayed on a periodic table.

        Args:
             elemental_data (dict): A dictionary with the element as a key and a
                value assigned to it, e.g. surface energy and frequency, etc.
                Elements missing in the elemental_data will be grey by default
                in the final table elemental_data={"Fe": 4.2, "O": 5.0}.
             cbar_label (string): Label of the colorbar. Default is "".
             cbar_label_size (float): Font size for the colorbar label. Default is 14.
             cmap_range (tuple): Minimum and maximum value of the colormap scale.
                If None, the colormap will autotmatically scale to the range of the
                data.
             show_plot (bool): Whether to show the heatmap. Default is False.
             value_format (str): Formatting string to show values. If None, no value
                is shown. Example: "%.4f" shows float to four decimals.
             cmap (string): Color scheme of the heatmap. Default is 'YlOrRd'.
                Refer to the matplotlib documentation for other options.
             blank_color (string): Color assigned for the missing elements in
                elemental_data. Default is "grey".
             max_row (integer): Maximum number of rows of the periodic table to be
                shown. Default is 9, which means the periodic table heat map covers
                the first 9 rows of elements.
        """

        # Convert primitive_elemental data in the form of numpy array for plotting.
        if cmap_range is not None:
            max_val = cmap_range[1]
            min_val = cmap_range[0]
        else:
            max_val = max(elemental_data.values())
            min_val = min(elemental_data.values())

        max_row = min(max_row, 9)

        if max_row <= 0:
            raise ValueError("The input argument 'max_row' must be positive!")

        value_table = np.empty((max_row, 18)) * np.nan
        blank_value = min_val - 0.01

        for el in Element:
            if el.row > max_row:
                continue
            value = elemental_data.get(el.symbol, blank_value)
            value_table[el.row - 1, el.group - 1] = value

        # Initialize the plt object
        import matplotlib.pyplot as plt
        fig, ax = plt.subplots()
        plt.gcf().set_size_inches(12, 8)

        # We set nan type values to masked values (ie blank spaces)
        data_mask = np.ma.masked_invalid(value_table.tolist())
        heatmap = ax.pcolor(data_mask, cmap=cmap, edgecolors='w', linewidths=1,
                            vmin=min_val - 0.001, vmax=max_val + 0.001)
        cbar = fig.colorbar(heatmap)

        # Grey out missing elements in input data
        cbar.cmap.set_under(blank_color)

        # Set the colorbar label and tick marks
        cbar.set_label(cbar_label, rotation=270, labelpad=25, size=cbar_label_size)
        cbar.ax.tick_params(labelsize=cbar_label_size)

        # Refine and make the table look nice
        ax.axis('off')
        ax.invert_yaxis()

        # Label each block with corresponding element and value
        for i, row in enumerate(value_table):
            for j, el in enumerate(row):
                if not np.isnan(el):
                    symbol = Element.from_row_and_group(i + 1, j + 1).symbol
                    plt.text(j + 0.5, i + 0.25, symbol,
                             horizontalalignment='center',
                             verticalalignment='center', fontsize=14)
                    if el != blank_value and value_format is not None:
                        plt.text(j + 0.5, i + 0.5, value_format % el,
                                 horizontalalignment='center',
                                 verticalalignment='center', fontsize=10)

        plt.tight_layout()

        if show_plot:
            plt.show()

        return plt

    def format_formula(formula):
        """
        Converts str of chemical formula into
        latex format for labelling purposes

        Args:
            formula (str): Chemical formula
        """

        formatted_formula = ""
        number_format = ""
        for i, s in enumerate(formula):
            if s.isdigit():
                if not number_format:
                    number_format = "_{"
                number_format += s
                if i == len(formula) - 1:
                    number_format += "}"
                    formatted_formula += number_format
            else:
                if number_format:
                    number_format += "}"
                    formatted_formula += number_format
                    number_format = ""
                formatted_formula += s

        return r"$%s$" % (formatted_formula)

    def van_arkel_triangle(list_of_materials, annotate=True):
        """
        A static method that generates a binary van Arkel-Ketelaar triangle to
            quantify the ionic, metallic and covalent character of a compound
            by plotting the electronegativity difference (y) vs average (x).
            See:
                A.E. van Arkel, Molecules and Crystals in Inorganic Chemistry,
                    Interscience, New York (1956)
            and
                J.A.A Ketelaar, Chemical Constitution (2nd edn.), An Introduction
                    to the Theory of the Chemical Bond, Elsevier, New York (1958)

        Args:
             list_of_materials (list): A list of computed entries of binary
                materials or a list of lists containing two elements (str).
             annotate (bool): Whether or not to lable the points on the
                triangle with reduced formula (if list of entries) or pair
                of elements (if list of list of str).
        """

        # F-Fr has the largest X difference. We set this
        # as our top corner of the triangle (most ionic)
        pt1 = np.array([(Element("F").X + Element("Fr").X) / 2,
                        abs(Element("F").X - Element("Fr").X)])
        # Cs-Fr has the lowest average X. We set this as our
        # bottom left corner of the triangle (most metallic)
        pt2 = np.array([(Element("Cs").X + Element("Fr").X) / 2,
                        abs(Element("Cs").X - Element("Fr").X)])
        # O-F has the highest average X. We set this as our
        # bottom right corner of the triangle (most covalent)
        pt3 = np.array([(Element("O").X + Element("F").X) / 2,
                        abs(Element("O").X - Element("F").X)])

        # get the parameters for the lines of the triangle
        d = np.array(pt1) - np.array(pt2)
        slope1 = d[1] / d[0]
        b1 = pt1[1] - slope1 * pt1[0]
        d = pt3 - pt1
        slope2 = d[1] / d[0]
        b2 = pt3[1] - slope2 * pt3[0]

        # Initialize the plt object
        import matplotlib.pyplot as plt

        # set labels and appropriate limits for plot
        plt.xlim(pt2[0] - 0.45, -b2 / slope2 + 0.45)
        plt.ylim(-0.45, pt1[1] + 0.45)
        plt.annotate("Ionic", xy=[pt1[0] - 0.3, pt1[1] + 0.05], fontsize=20)
        plt.annotate("Covalent", xy=[-b2 / slope2 - 0.65, -0.4], fontsize=20)
        plt.annotate("Metallic", xy=[pt2[0] - 0.4, -0.4], fontsize=20)
        plt.xlabel(r"$\frac{\chi_{A}+\chi_{B}}{2}$", fontsize=25)
        plt.ylabel(r"$|\chi_{A}-\chi_{B}|$", fontsize=25)

        # Set the lines of the triangle
        chi_list = [el.X for el in Element]
        plt.plot([min(chi_list), pt1[0]], [slope1 * min(chi_list) + b1, pt1[1]], 'k-', linewidth=3)
        plt.plot([pt1[0], -b2 / slope2], [pt1[1], 0], 'k-', linewidth=3)
        plt.plot([min(chi_list), -b2 / slope2], [0, 0], 'k-', linewidth=3)
        plt.xticks(fontsize=15)
        plt.yticks(fontsize=15)

        # Shade with appropriate colors corresponding to ionic, metallci and covalent
        ax = plt.gca()
        # ionic filling
        ax.fill_between([min(chi_list), pt1[0]],
                        [slope1 * min(chi_list) + b1, pt1[1]], facecolor=[1, 1, 0],
                        zorder=-5, edgecolor=[1, 1, 0])
        ax.fill_between([pt1[0], -b2 / slope2],
                        [pt1[1], slope2 * min(chi_list) - b1], facecolor=[1, 1, 0],
                        zorder=-5, edgecolor=[1, 1, 0])
        # metal filling
        XPt = Element("Pt").X
        ax.fill_between([min(chi_list), (XPt + min(chi_list)) / 2],
                        [0, slope1 * (XPt + min(chi_list)) / 2 + b1],
                        facecolor=[1, 0, 0], zorder=-3, alpha=0.8)
        ax.fill_between([(XPt + min(chi_list)) / 2, XPt],
                        [slope1 * ((XPt + min(chi_list)) / 2) + b1, 0],
                        facecolor=[1, 0, 0], zorder=-3, alpha=0.8)
        # covalent filling
        ax.fill_between([(XPt + min(chi_list)) / 2, ((XPt + min(chi_list)) / 2 + -b2 / slope2) / 2],
                        [0, slope2 * (((XPt + min(chi_list)) / 2 + -b2 / slope2) / 2) + b2],
                        facecolor=[0, 1, 0], zorder=-4, alpha=0.8)
        ax.fill_between([((XPt + min(chi_list)) / 2 + -b2 / slope2) / 2, -b2 / slope2],
                        [slope2 * (((XPt + min(chi_list)) / 2 + -b2 / slope2) / 2) + b2, 0],
                        facecolor=[0, 1, 0], zorder=-4, alpha=0.8)

        # Label the triangle with datapoints
        for entry in list_of_materials:
            if type(entry).__name__ not in ['ComputedEntry', 'ComputedStructureEntry']:
                X_pair = [Element(el).X for el in entry]
                formatted_formula = "%s-%s" % tuple(entry)
            else:
                X_pair = [Element(el).X for el in entry.composition.as_dict().keys()]
                formatted_formula = format_formula(entry.composition.reduced_formula)
            plt.scatter(np.mean(X_pair), abs(X_pair[0] - X_pair[1]), c='b', s=100)
            if annotate:
                plt.annotate(formatted_formula, fontsize=15,
                             xy=[np.mean(X_pair) + 0.005, abs(X_pair[0] - X_pair[1])])

        plt.tight_layout()
        return plt

    def get_ax_fig_plt(ax=None, **kwargs):
        """
        Helper function used in plot functions supporting an optional Axes argument.
        If ax is None, we build the `matplotlib` figure and create the Axes else
        we return the current active figure.

        Args:
            kwargs: keyword arguments are passed to plt.figure if ax is not None.

        Returns:
            ax: :class:`Axes` object
            figure: matplotlib figure
            plt: matplotlib pyplot module.
        """
        import matplotlib.pyplot as plt
        if ax is None:
            fig = plt.figure(**kwargs)
            ax = fig.add_subplot(1, 1, 1)
        else:
            fig = plt.gcf()

        return ax, fig, plt

    def get_ax3d_fig_plt(ax=None, **kwargs):
        """
        Helper function used in plot functions supporting an optional Axes3D
        argument. If ax is None, we build the `matplotlib` figure and create the
        Axes3D else we return the current active figure.

        Args:
            kwargs: keyword arguments are passed to plt.figure if ax is not None.

        Returns:
            ax: :class:`Axes` object
            figure: matplotlib figure
            plt: matplotlib pyplot module.
        """
        import matplotlib.pyplot as plt
        from mpl_toolkits.mplot3d import axes3d
        if ax is None:
            fig = plt.figure(**kwargs)
            ax = axes3d.Axes3D(fig)
        else:
            fig = plt.gcf()

        return ax, fig, plt

    def get_axarray_fig_plt(ax_array, nrows=1, ncols=1, sharex=False, sharey=False,
                            squeeze=True, subplot_kw=None, gridspec_kw=None,
                            **fig_kw):
        """
        Helper function used in plot functions that accept an optional array of Axes
        as argument. If ax_array is None, we build the `matplotlib` figure and
        create the array of Axes by calling plt.subplots else we return the
        current active figure.

        Returns:
            ax: Array of :class:`Axes` objects
            figure: matplotlib figure
            plt: matplotlib pyplot module.
        """
        import matplotlib.pyplot as plt

        if ax_array is None:
            fig, ax_array = plt.subplots(nrows=nrows, ncols=ncols, sharex=sharex,
                                         sharey=sharey, squeeze=squeeze,
                                         subplot_kw=subplot_kw,
                                         gridspec_kw=gridspec_kw, **fig_kw)
        else:
            fig = plt.gcf()
            ax_array = np.reshape(np.array(ax_array), (nrows, ncols))
            if squeeze:
                if ax_array.size == 1:
                    ax_array = ax_array[0]
                elif any(s == 1 for s in ax_array.shape):
                    ax_array = ax_array.ravel()

        return ax_array, fig, plt

    def add_fig_kwargs(func):
        """
        Decorator that adds keyword arguments for functions returning matplotlib
        figures.

        The function should return either a matplotlib figure or None to signal
        some sort of error/unexpected event.
        See doc string below for the list of supported options.
        """
        from functools import wraps

        @wraps(func)
        def wrapper(*args, **kwargs):
            # pop the kwds used by the decorator.
            title = kwargs.pop("title", None)
            size_kwargs = kwargs.pop("size_kwargs", None)
            show = kwargs.pop("show", True)
            savefig = kwargs.pop("savefig", None)
            tight_layout = kwargs.pop("tight_layout", False)
            ax_grid = kwargs.pop("ax_grid", None)
            ax_annotate = kwargs.pop("ax_annotate", None)
            fig_close = kwargs.pop("fig_close", False)

            # Call func and return immediately if None is returned.
            fig = func(*args, **kwargs)
            if fig is None:
                return fig

            # Operate on matplotlib figure.
            if title is not None:
                fig.suptitle(title)

            if size_kwargs is not None:
                fig.set_size_inches(size_kwargs.pop("w"), size_kwargs.pop("h"),
                                    **size_kwargs)

            if ax_grid is not None:
                for ax in fig.axes:
                    ax.grid(bool(ax_grid))

            if ax_annotate:
                from string import ascii_letters
                tags = ascii_letters
                if len(fig.axes) > len(tags):
                    tags = (1 + len(ascii_letters) // len(fig.axes)) * ascii_letters
                for ax, tag in zip(fig.axes, tags):
                    ax.annotate("(%s)" % tag, xy=(0.05, 0.95), xycoords="axes fraction")

            if tight_layout:
                try:
                    fig.tight_layout()
                except Exception as exc:
                    # For some unknown reason, this problem shows up only on travis.
                    # https://stackoverflow.com/questions/22708888/valueerror-when-using-matplotlib-tight-layout
                    print("Ignoring Exception raised by fig.tight_layout\n", str(exc))

            if savefig:
                fig.savefig(savefig)

            import matplotlib.pyplot as plt
            if show:
                plt.show()
            if fig_close:
                plt.close(fig=fig)

            return fig

        # Add docstring to the decorated method.
        s = "\n\n" + """\
            Keyword arguments controlling the display of the figure:

            ================  ====================================================
            kwargs            Meaning
            ================  ====================================================
            title             Title of the plot (Default: None).
            show              True to show the figure (default: True).
            savefig           "abc.png" or "abc.eps" to save the figure to a file.
            size_kwargs       Dictionary with options passed to fig.set_size_inches
                              e.g. size_kwargs=dict(w=3, h=4)
            tight_layout      True to call fig.tight_layout (default: False)
            ax_grid           True (False) to add (remove) grid from all axes in fig.
                              Default: None i.e. fig is left unchanged.
            ax_annotate       Add labels to  subplots e.g. (a), (b).
                              Default: False
            fig_close         Close figure. Default: False.
            ================  ====================================================

    """

        if wrapper.__doc__ is not None:
            # Add s at the end of the docstring.
            wrapper.__doc__ += "\n" + s
        else:
            # Use s
            wrapper.__doc__ = s

        return wrapper