GLDF 0.9.0__py3-none-any.whl

GLDF/bridges/tigramite_plotting_modified.py

@@ -0,0 +1,4764 @@
+"""Tigramite plotting package."""
+
+# Author: Jakob Runge <jakob@jakob-runge.com>
+#
+# License: GNU General Public License v3.0
+
+import numpy as np
+import json, warnings, os, pathlib
+import matplotlib
+import networkx as nx
+from matplotlib.colors import ListedColormap
+import matplotlib.transforms as transforms
+from matplotlib import pyplot, ticker
+from matplotlib.ticker import FormatStrFormatter
+import matplotlib.patches as mpatches
+from matplotlib.collections import PatchCollection
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+import sys
+from operator import sub
+import tigramite.data_processing as pp
+from copy import deepcopy
+import matplotlib.path as mpath
+import matplotlib.patheffects as PathEffects
+from mpl_toolkits.axisartist.axislines import Axes
+import csv
+
+
+# TODO: Add proper docstrings to internal functions...
+
+
+def _par_corr_trafo(cmi):
+    """Transformation of CMI to partial correlation scale."""
+
+    # Set negative values to small positive number
+    # (zero would be interpreted as non-significant in some functions)
+    if np.ndim(cmi) == 0:
+        if cmi < 0.0:
+            cmi = 1e-8
+    else:
+        cmi[cmi < 0.0] = 1e-8
+
+    return np.sqrt(1.0 - np.exp(-2.0 * cmi))
+
+
+def _par_corr_to_cmi(par_corr):
+    """Transformation of partial correlation to CMI scale."""
+
+    return -0.5 * np.log(1.0 - par_corr ** 2)
+
+
+def _myround(x, base=5, round_mode="updown"):
+    """Rounds x to a float with precision base."""
+
+    if round_mode == "updown":
+        return base * round(float(x) / base)
+    elif round_mode == "down":
+        return base * np.floor(float(x) / base)
+    elif round_mode == "up":
+        return base * np.ceil(float(x) / base)
+
+    return base * round(float(x) / base)
+
+
+def _make_nice_axes(ax, where=None, skip=1, color=None):
+    """Makes nice axes."""
+
+    if where is None:
+        where = ["left", "bottom"]
+    if color is None:
+        color = {"left": "black", "right": "black", "bottom": "black", "top": "black"}
+
+    if type(skip) == int:
+        skip_x = skip_y = skip
+    else:
+        skip_x = skip[0]
+        skip_y = skip[1]
+
+    for loc, spine in ax.spines.items():
+        if loc in where:
+            spine.set_position(("outward", 5))  # outward by 10 points
+            spine.set_color(color[loc])
+            if loc == "left" or loc == "right":
+                pyplot.setp(ax.get_yticklines(), color=color[loc])
+                pyplot.setp(ax.get_yticklabels(), color=color[loc])
+            if loc == "top" or loc == "bottom":
+                pyplot.setp(ax.get_xticklines(), color=color[loc])
+        elif loc in [
+            item for item in ["left", "bottom", "right", "top"] if item not in where
+        ]:
+            spine.set_color("none")  # don't draw spine
+        else:
+            raise ValueError("unknown spine location: %s" % loc)
+
+    # ax.xaxis.get_major_formatter().set_useOffset(False)
+
+    # turn off ticks where there is no spine
+    if "top" in where and "bottom" not in where:
+        ax.xaxis.set_ticks_position("top")
+        if skip_x > 1:
+            ax.set_xticks(ax.get_xticks()[::skip_x])
+    elif "bottom" in where:
+        ax.xaxis.set_ticks_position("bottom")
+        if skip_x > 1:
+            ax.set_xticks(ax.get_xticks()[::skip_x])
+    else:
+        ax.xaxis.set_ticks_position("none")
+        ax.xaxis.set_ticklabels([])
+    if "right" in where and "left" not in where:
+        ax.yaxis.set_ticks_position("right")
+        if skip_y > 1:
+            ax.set_yticks(ax.get_yticks()[::skip_y])
+    elif "left" in where:
+        ax.yaxis.set_ticks_position("left")
+        if skip_y > 1:
+            ax.set_yticks(ax.get_yticks()[::skip_y])
+    else:
+        ax.yaxis.set_ticks_position("none")
+        ax.yaxis.set_ticklabels([])
+
+    ax.patch.set_alpha(0.0)
+
+
+def _get_absmax(val_matrix):
+    """Get value at absolute maximum in lag function array.
+    For an (N, N, tau)-array this comutes the lag of the absolute maximum
+    along the tau-axis and stores the (positive or negative) value in
+    the (N,N)-array absmax."""
+
+    absmax_indices = np.abs(val_matrix).argmax(axis=2)
+    i, j = np.indices(val_matrix.shape[:2])
+
+    return val_matrix[i, j, absmax_indices]
+
+
+def _add_timeseries(
+        dataframe,
+        fig_axes,
+        grey_masked_samples=False,
+        show_meanline=False,
+        data_linewidth=1.0,
+        color="black",
+        alpha=1.,
+        grey_alpha=1.0,
+        selected_dataset=0,
+        selected_variables=None,
+):
+    """Adds a time series plot to an axis.
+    Plot of dataseries is added to axis. Allows for proper visualization of
+    masked data.
+
+    Parameters
+    ----------
+    fig : figure instance
+        Figure instance.
+    axes : axis instance
+        Either gridded axis object or single axis instance.
+    grey_masked_samples : bool, optional (default: False)
+        Whether to mark masked samples by grey fills ('fill') or grey data
+        ('data').
+    show_meanline : bool
+        Show mean of data as horizontal line.
+    data_linewidth : float, optional (default: 1.)
+        Linewidth.
+    color : str, optional (default: black)
+        Line color.
+    alpha : float
+        Alpha opacity.
+    grey_alpha : float, optional (default: 1.)
+        Opacity of fill_between.
+    selected_dataset : int, optional (default: 0)
+        In case of multiple datasets in dataframe, plot this one.
+    selected_variables : list, optional (default: None)
+        List of variables which to plot.
+    """
+    fig, axes = fig_axes
+
+    # Read in all attributes from dataframe
+    data = dataframe.values[selected_dataset]
+    if dataframe.mask is not None:
+        mask = dataframe.mask[selected_dataset]
+    else:
+        mask = None
+
+    missing_flag = dataframe.missing_flag
+    time = dataframe.datatime[selected_dataset]
+    T = len(time)
+
+    if selected_variables is None:
+        selected_variables = list(range(dataframe.N))
+
+    nb_components = sum([len(dataframe.vector_vars[var]) for var in selected_variables])
+
+    for j in range(nb_components):
+
+        ax = axes[j]
+        dataseries = data[:, j]
+
+        if missing_flag is not None:
+            dataseries_nomissing = np.ma.masked_where(
+                dataseries == missing_flag, dataseries
+            )
+        else:
+            dataseries_nomissing = np.ma.masked_where(
+                np.zeros(dataseries.shape), dataseries
+            )
+
+
+        if mask is not None:
+            maskseries = mask[:, j]
+
+            maskdata = np.ma.masked_where(maskseries, dataseries_nomissing)
+
+            if grey_masked_samples == "fill":
+                ax.fill_between(
+                    time,
+                    maskdata.min(),
+                    maskdata.max(),
+                    where=maskseries,
+                    color="grey",
+                    interpolate=True,
+                    linewidth=0.0,
+                    alpha=grey_alpha,
+                )
+            elif grey_masked_samples == "data":
+                ax.plot(
+                    time,
+                    dataseries_nomissing,
+                    color="grey",
+                    marker=".",
+                    markersize=data_linewidth,
+                    linewidth=data_linewidth,
+                    clip_on=False,
+                    alpha=grey_alpha,
+                )
+            if show_meanline:
+                ax.plot(time, maskdata.mean() * np.ones(T), lw=data_linewidth / 2., color=color)
+
+            ax.plot(
+                time,
+                maskdata,
+                color=color,
+                linewidth=data_linewidth,
+                marker=".",
+                markersize=data_linewidth,
+                clip_on=False,
+                alpha=alpha,
+            )
+        else:
+            if show_meanline:
+                ax.plot(time, dataseries_nomissing.mean() * np.ones(T), lw=data_linewidth / 2., color=color)
+
+            ax.plot(
+                time,
+                dataseries_nomissing,
+                color=color,
+                linewidth=data_linewidth,
+                clip_on=False,
+                alpha=alpha,
+            )
+
+
+def plot_timeseries(
+        dataframe=None,
+        save_name=None,
+        fig_axes=None,
+        figsize=None,
+        var_units=None,
+        time_label="",
+        grey_masked_samples=False,
+        show_meanline=False,
+        data_linewidth=1.0,
+        skip_ticks_data_x=1,
+        skip_ticks_data_y=1,
+        label_fontsize=10,
+        color='black',
+        alpha=1.,
+        tick_label_size=6,
+        selected_dataset=0,
+        adjust_plot=True,
+        selected_variables=None,
+):
+    """Create and save figure of stacked panels with time series.
+
+    Parameters
+    ----------
+    dataframe : data object, optional
+        This is the Tigramite dataframe object. It has the attributes
+        dataframe.values yielding a np array of shape (observations T,
+        variables N) and optionally a mask of the same shape.
+    save_name : str, optional (default: None)
+        Name of figure file to save figure. If None, figure is shown in window.
+    fig_axes : subplots instance, optional (default: None)
+        Figure and axes instance. If None they are created as
+        fig, axes = pyplot.subplots(N,...)
+    figsize : tuple of floats, optional (default: None)
+        Figure size if new figure is created. If None, default pyplot figsize
+        is used.
+    var_units : list of str, optional (default: None)
+        Units of variables.
+    time_label : str, optional (default: '')
+        Label of time axis.
+    grey_masked_samples : bool, optional (default: False)
+        Whether to mark masked samples by grey fills ('fill') or grey data
+        ('data').
+    show_meanline : bool, optional (default: False)
+        Whether to plot a horizontal line at the mean.
+    data_linewidth : float, optional (default: 1.)
+        Linewidth.
+    skip_ticks_data_x : int, optional (default: 1)
+        Skip every other tickmark.
+    skip_ticks_data_y : int, optional (default: 2)
+        Skip every other tickmark.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of variable labels.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    color : str, optional (default: black)
+        Line color.
+    alpha : float
+        Alpha opacity.
+    selected_dataset : int, optional (default: 0)
+        In case of multiple datasets in dataframe, plot this one.
+    selected_variables : list, optional (default: None)
+        List of variables which to plot.
+    """
+
+    var_names = dataframe.var_names
+    time = dataframe.datatime[selected_dataset]
+
+    N = dataframe.N
+
+    if selected_variables is None:
+        selected_variables = list(range(N))
+
+    nb_components_per_var = [len(dataframe.vector_vars[var]) for var in selected_variables]
+    N_index = [sum(nb_components_per_var[:i]) for i, el in enumerate(nb_components_per_var)]
+    nb_components = sum(nb_components_per_var)
+
+    if var_units is None:
+        var_units = ["" for i in range(N)]
+
+    if fig_axes is None:
+        fig, axes = pyplot.subplots(nb_components, sharex=True, figsize=figsize)
+    else:
+        fig, axes = fig_axes
+
+    if adjust_plot:
+        for i in range(nb_components):
+
+            ax = axes[i]
+
+            if (i == nb_components - 1):
+                _make_nice_axes(
+                    ax, where=["left", "bottom"], skip=(skip_ticks_data_x, skip_ticks_data_y)
+                )
+                ax.set_xlabel(r"%s" % time_label, fontsize=label_fontsize)
+            else:
+                _make_nice_axes(ax, where=["left"], skip=(skip_ticks_data_x, skip_ticks_data_y))
+            # ax.get_xaxis().get_major_formatter().set_useOffset(False)
+
+            ax.xaxis.set_major_formatter(FormatStrFormatter("%.0f"))
+            ax.label_outer()
+
+            ax.set_xlim(time[0], time[-1])
+
+            # trans = transforms.blended_transform_factory(fig.transFigure, ax.transAxes)
+            if i in N_index:
+                if var_units[N_index.index(i)]:
+                    ax.set_ylabel(r"%s [%s]" % (var_names[N_index.index(i)], var_units[N_index.index(i)]),
+                                  fontsize=label_fontsize)
+                else:
+                    ax.set_ylabel(r"%s" % (var_names[N_index.index(i)]), fontsize=label_fontsize)
+
+            ax.tick_params(axis='both', which='major', labelsize=tick_label_size)
+            # ax.tick_params(axis='both', which='minor', labelsize=tick_label_size)
+
+    _add_timeseries(
+        dataframe=dataframe,
+        fig_axes=(fig, axes),
+        grey_masked_samples=grey_masked_samples,
+        show_meanline=show_meanline,
+        data_linewidth=data_linewidth,
+        color=color,
+        selected_dataset=selected_dataset,
+        alpha=alpha,
+        selected_variables=selected_variables
+    )
+
+    if adjust_plot:
+        fig.subplots_adjust(bottom=0.15, top=0.9, left=0.15, right=0.95, hspace=0.3)
+        pyplot.tight_layout()
+
+    if save_name is not None:
+        fig.savefig(save_name)
+
+    return fig, axes
+
+
+def plot_lagfuncs(val_matrix,
+                  name=None,
+                  setup_args={},
+                  add_lagfunc_args={}):
+    """Wrapper helper function to plot lag functions.
+    Sets up the matrix object and plots the lagfunction, see parameters in
+    setup_matrix and add_lagfuncs.
+
+    Parameters
+    ----------
+    val_matrix : array_like
+        Matrix of shape (N, N, tau_max+1) containing test statistic values.
+    name : str, optional (default: None)
+        File name. If None, figure is shown in window.
+    setup_args : dict
+        Arguments for setting up the lag function matrix, see doc of
+        setup_matrix.
+    add_lagfunc_args : dict
+        Arguments for adding a lag function matrix, see doc of add_lagfuncs.
+
+    Returns
+    -------
+    matrix : object
+        Further lag functions can be overlaid using the
+        matrix.add_lagfuncs(val_matrix) function.
+    """
+
+    N, N, tau_max_plusone = val_matrix.shape
+    tau_max = tau_max_plusone - 1
+
+    matrix = setup_matrix(N=N, tau_max=tau_max, **setup_args)
+    matrix.add_lagfuncs(val_matrix=val_matrix, **add_lagfunc_args)
+    matrix.savefig(name=name)
+
+    return matrix
+
+
+class setup_matrix:
+    """Create matrix of lag function panels.
+    Class to setup figure object. The function add_lagfuncs(...) allows to plot
+    the val_matrix of shape (N, N, tau_max+1). Multiple lagfunctions can be
+    overlaid for comparison.
+
+    Parameters
+    ----------
+    N : int
+        Number of variables
+    tau_max : int
+        Maximum time lag.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    figsize : tuple of floats, optional (default: None)
+        Figure size if new figure is created. If None, default pyplot figsize
+        is used.
+    minimum : float, optional (default: -1.)
+        Lower y-axis limit.
+    maximum : float, optional (default: 1.)
+        Upper y-axis limit.
+    label_space_left : float, optional (default: 0.1)
+        Fraction of horizontal figure space to allocate left of plot for labels.
+    label_space_top : float, optional (default: 0.05)
+        Fraction of vertical figure space to allocate top of plot for labels.
+    legend_width : float, optional (default: 0.15)
+        Fraction of horizontal figure space to allocate right of plot for
+        legend.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    x_base : float, optional (default: 1.)
+        x-tick intervals to show.
+    y_base : float, optional (default: .4)
+        y-tick intervals to show.
+    plot_gridlines : bool, optional (default: False)
+        Whether to show a grid.
+    lag_units : str, optional (default: '')
+    lag_array : array, optional (default: None)
+        Optional specification of lags overwriting np.arange(0, tau_max+1)
+    label_fontsize : int, optional (default: 10)
+        Fontsize of variable labels.
+    """
+
+    def __init__(
+        self,
+        N,
+        tau_max,
+        var_names=None,
+        figsize=None,
+        minimum=-1,
+        maximum=1,
+        label_space_left=0.1,
+        label_space_top=0.05,
+        legend_width=0.15,
+        legend_fontsize=10,
+        x_base=1.0,
+        y_base=0.5,
+        tick_label_size=6,
+        plot_gridlines=False,
+        lag_units="",
+        lag_array=None,
+        label_fontsize=10,
+    ):
+
+        self.tau_max = tau_max
+
+        self.labels = []
+        self.lag_units = lag_units
+        # if lag_array is None:
+        #     self.lag_array = np.arange(0, self.tau_max + 1)
+        # else:
+        self.lag_array = lag_array
+        if x_base is None:
+            self.x_base = 1
+        else:
+            self.x_base = x_base
+
+        self.legend_width = legend_width
+        self.legend_fontsize = legend_fontsize
+
+        self.label_space_left = label_space_left
+        self.label_space_top = label_space_top
+        self.label_fontsize = label_fontsize
+
+        self.fig = pyplot.figure(figsize=figsize)
+
+        self.axes_dict = {}
+
+        if var_names is None:
+            var_names = range(N)
+
+        plot_index = 1
+        for i in range(N):
+            for j in range(N):
+                self.axes_dict[(i, j)] = self.fig.add_subplot(N, N, plot_index)
+                # Plot process labels
+                if j == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.fig.transFigure, self.axes_dict[(i, j)].transAxes
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.01,
+                        0.5,
+                        "%s" % str(var_names[i]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="left",
+                        verticalalignment="center",
+                        transform=trans,
+                    )
+                if i == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.axes_dict[(i, j)].transAxes, self.fig.transFigure
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.5,
+                        0.99,
+                        r"${\to}$ " + "%s" % str(var_names[j]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="center",
+                        verticalalignment="top",
+                        transform=trans,
+                    )
+
+                # Make nice axis
+                _make_nice_axes(
+                    self.axes_dict[(i, j)], where=["left", "bottom"], skip=(1, 1)
+                )
+                if x_base is not None:
+                    self.axes_dict[(i, j)].xaxis.set_major_locator(
+                        ticker.FixedLocator(np.arange(0, self.tau_max + 1, x_base))
+                    )
+                    if x_base / 2.0 % 1 == 0:
+                        self.axes_dict[(i, j)].xaxis.set_minor_locator(
+                            ticker.FixedLocator(
+                                np.arange(0, self.tau_max + 1, x_base / 2.0)
+                            )
+                        )
+                if y_base is not None:
+                    self.axes_dict[(i, j)].yaxis.set_major_locator(
+                        ticker.FixedLocator(
+                            np.arange(
+                                _myround(minimum, y_base, "down"),
+                                _myround(maximum, y_base, "up") + y_base,
+                                y_base,
+                            )
+                        )
+                    )
+                    self.axes_dict[(i, j)].yaxis.set_minor_locator(
+                        ticker.FixedLocator(
+                            np.arange(
+                                _myround(minimum, y_base, "down"),
+                                _myround(maximum, y_base, "up") + y_base,
+                                y_base / 2.0,
+                            )
+                        )
+                    )
+
+                    self.axes_dict[(i, j)].set_ylim(
+                        _myround(minimum, y_base, "down"),
+                        _myround(maximum, y_base, "up"),
+                    )
+                if j != 0:
+                    self.axes_dict[(i, j)].get_yaxis().set_ticklabels([])
+                self.axes_dict[(i, j)].set_xlim(0, self.tau_max)
+                if plot_gridlines:
+                    self.axes_dict[(i, j)].grid(
+                        True,
+                        which="major",
+                        color="black",
+                        linestyle="dotted",
+                        dashes=(1, 1),
+                        linewidth=0.05,
+                        zorder=-5,
+                    )
+                self.axes_dict[(i, j)].tick_params(axis='both', which='major', labelsize=tick_label_size)
+                self.axes_dict[(i, j)].tick_params(axis='both', which='minor', labelsize=tick_label_size)
+
+                plot_index += 1
+
+    def add_lagfuncs(
+        self,
+        val_matrix,
+        sig_thres=None,
+        conf_matrix=None,
+        color="black",
+        label=None,
+        two_sided_thres=True,
+        marker=".",
+        markersize=5,
+        alpha=1.0,
+    ):
+        """Add lag function plot from val_matrix array.
+
+        Parameters
+        ----------
+        val_matrix : array_like
+            Matrix of shape (N, N, tau_max+1) containing test statistic values.
+        sig_thres : array-like, optional (default: None)
+            Matrix of significance thresholds. Must be of same shape as
+            val_matrix.
+        conf_matrix : array-like, optional (default: None)
+            Matrix of shape (, N, tau_max+1, 2) containing confidence bounds.
+        color : str, optional (default: 'black')
+            Line color.
+        label : str
+            Test statistic label.
+        two_sided_thres : bool, optional (default: True)
+            Whether to draw sig_thres for pos. and neg. values.
+        marker : matplotlib marker symbol, optional (default: '.')
+            Marker.
+        markersize : int, optional (default: 5)
+            Marker size.
+        alpha : float, optional (default: 1.)
+            Opacity.
+        """
+
+        if label is not None:
+            self.labels.append((label, color, marker, markersize, alpha))
+
+        for ij in list(self.axes_dict):
+            i = ij[0]
+            j = ij[1]
+            maskedres = np.copy(val_matrix[i, j, int(i == j) :])
+            self.axes_dict[(i, j)].plot(
+                range(int(i == j), self.tau_max + 1),
+                maskedres,
+                linestyle="",
+                color=color,
+                marker=marker,
+                markersize=markersize,
+                alpha=alpha,
+                clip_on=False,
+            )
+            if conf_matrix is not None:
+                maskedconfres = np.copy(conf_matrix[i, j, int(i == j) :])
+                self.axes_dict[(i, j)].plot(
+                    range(int(i == j), self.tau_max + 1),
+                    maskedconfres[:, 0],
+                    linestyle="",
+                    color=color,
+                    marker="_",
+                    markersize=markersize - 2,
+                    alpha=alpha,
+                    clip_on=False,
+                )
+                self.axes_dict[(i, j)].plot(
+                    range(int(i == j), self.tau_max + 1),
+                    maskedconfres[:, 1],
+                    linestyle="",
+                    color=color,
+                    marker="_",
+                    markersize=markersize - 2,
+                    alpha=alpha,
+                    clip_on=False,
+                )
+
+            self.axes_dict[(i, j)].plot(
+                range(int(i == j), self.tau_max + 1),
+                np.zeros(self.tau_max + 1 - int(i == j)),
+                color="black",
+                linestyle="dotted",
+                linewidth=0.1,
+            )
+
+            if sig_thres is not None:
+                maskedsigres = sig_thres[i, j, int(i == j) :]
+
+                self.axes_dict[(i, j)].plot(
+                    range(int(i == j), self.tau_max + 1),
+                    maskedsigres,
+                    color=color,
+                    linestyle="solid",
+                    linewidth=0.1,
+                    alpha=alpha,
+                )
+                if two_sided_thres:
+                    self.axes_dict[(i, j)].plot(
+                        range(int(i == j), self.tau_max + 1),
+                        -sig_thres[i, j, int(i == j) :],
+                        color=color,
+                        linestyle="solid",
+                        linewidth=0.1,
+                        alpha=alpha,
+                    )
+        # pyplot.tight_layout()
+
+    def savefig(self, name=None):
+        """Save matrix figure.
+
+        Parameters
+        ----------
+        name : str, optional (default: None)
+            File name. If None, figure is shown in window.
+        """
+
+        # Trick to plot legend
+        if len(self.labels) > 0:
+            axlegend = self.fig.add_subplot(111, frameon=False)
+            axlegend.spines["left"].set_color("none")
+            axlegend.spines["right"].set_color("none")
+            axlegend.spines["bottom"].set_color("none")
+            axlegend.spines["top"].set_color("none")
+            axlegend.set_xticks([])
+            axlegend.set_yticks([])
+
+            # self.labels.append((label, color, marker, markersize, alpha))
+            for item in self.labels:
+                label = item[0]
+                color = item[1]
+                marker = item[2]
+                markersize = item[3]
+                alpha = item[4]
+
+                axlegend.plot(
+                    [],
+                    [],
+                    linestyle="",
+                    color=color,
+                    marker=marker,
+                    markersize=markersize,
+                    label=label,
+                    alpha=alpha,
+                )
+            axlegend.legend(
+                loc="upper left",
+                ncol=1,
+                bbox_to_anchor=(1.05, 0.0, 0.1, 1.0),
+                borderaxespad=0,
+                fontsize=self.legend_fontsize,
+            ).draw_frame(False)
+
+            self.fig.subplots_adjust(
+                left=self.label_space_left,
+                right=1.0 - self.legend_width,
+                top=1.0 - self.label_space_top,
+                hspace=0.35,
+                wspace=0.35,
+            )
+            pyplot.figtext(
+                0.5,
+                0.01,
+                r"lag $\tau$ [%s]" % self.lag_units,
+                horizontalalignment="center",
+                fontsize=self.label_fontsize,
+            )
+        else:
+            self.fig.subplots_adjust(
+                left=self.label_space_left,
+                right=0.95,
+                top=1.0 - self.label_space_top,
+                hspace=0.35,
+                wspace=0.35,
+            )
+            pyplot.figtext(
+                0.55,
+                0.01,
+                r"lag $\tau$ [%s]" % self.lag_units,
+                horizontalalignment="center",
+                fontsize=self.label_fontsize,
+            )
+
+        if self.lag_array is not None:
+            assert self.lag_array.shape == np.arange(self.tau_max + 1).shape
+            for ij in list(self.axes_dict):
+                i = ij[0]
+                j = ij[1]
+                self.axes_dict[(i, j)].set_xticklabels(self.lag_array[:: self.x_base])
+
+        if name is not None:
+            self.fig.savefig(name)
+        else:
+            pyplot.show()
+
+
+
+def plot_scatterplots(dataframe,
+                      name=None,
+                      setup_args={},
+                      add_scatterplot_args={},
+                      selected_dataset=0):
+    """Wrapper helper function to plot scatter plots.
+    Sets up the matrix object and plots the scatter plots, see parameters in
+    setup_scatter_matrix and add_scatterplot.
+
+    Parameters
+    ----------
+    dataframe : data object
+        Tigramite dataframe object. It must have the attributes dataframe.values
+        yielding a numpy array of shape (observations T, variables N) and
+        optionally a mask of the same shape and a missing values flag.
+    name : str, optional (default: None)
+        File name. If None, figure is shown in window.
+    setup_args : dict
+        Arguments for setting up the scatter plot matrix, see doc of
+        setup_scatter_matrix.
+    add_scatterplot_args : dict
+        Arguments for adding a scatter plot matrix.
+    selected_dataset : int, optional (default: 0)
+        In case of multiple datasets in dataframe, plot this one.
+
+    Returns
+    -------
+    matrix : object
+        Further scatter plot can be overlaid using the
+        matrix.add_scatterplot function.
+    """
+
+    N = dataframe.N
+
+    matrix = setup_scatter_matrix(N=N, var_names=dataframe.var_names, **setup_args)
+    matrix.add_scatterplot(dataframe=dataframe, selected_dataset=selected_dataset, **add_scatterplot_args)
+    matrix.adjustfig(name=name)
+
+
+    return matrix
+
+
+class setup_scatter_matrix:
+    """Create matrix of scatter plot panels.
+    Class to setup figure object. The function add_scatterplot allows to plot
+    scatterplots of variables in the dataframe. Multiple scatter plots can be
+    overlaid for comparison.
+
+    Parameters
+    ----------
+    N : int
+        Number of variables
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    figsize : tuple of floats, optional (default: None)
+        Figure size if new figure is created. If None, default pyplot figsize
+        is used.
+    label_space_left : float, optional (default: 0.1)
+        Fraction of horizontal figure space to allocate left of plot for labels.
+    label_space_top : float, optional (default: 0.05)
+        Fraction of vertical figure space to allocate top of plot for labels.
+    legend_width : float, optional (default: 0.15)
+        Fraction of horizontal figure space to allocate right of plot for
+        legend.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    plot_gridlines : bool, optional (default: False)
+        Whether to show a grid.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of variable labels.
+    """
+
+    def __init__(
+        self,
+        N,
+        var_names=None,
+        figsize=None,
+        label_space_left=0.1,
+        label_space_top=0.05,
+        legend_width=0.15,
+        legend_fontsize=10,
+        plot_gridlines=False,
+        tick_label_size=6,
+        label_fontsize=10,
+    ):
+
+        self.labels = []
+
+        self.legend_width = legend_width
+        self.legend_fontsize = legend_fontsize
+
+        self.label_space_left = label_space_left
+        self.label_space_top = label_space_top
+        self.label_fontsize = label_fontsize
+
+        self.fig = pyplot.figure(figsize=figsize)
+
+        self.axes_dict = {}
+
+        if var_names is None:
+            var_names = range(N)
+
+        plot_index = 1
+        for i in range(N):
+            for j in range(N):
+                self.axes_dict[(i, j)] = self.fig.add_subplot(N, N, plot_index, axes_class=Axes)
+                # Plot process labels
+                if j == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.fig.transFigure, self.axes_dict[(i, j)].transAxes
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.01,
+                        0.5,
+                        "%s" % str(var_names[i]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="left",
+                        verticalalignment="center",
+                        transform=trans,
+                    )
+                if i == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.axes_dict[(i, j)].transAxes, self.fig.transFigure
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.5,
+                        0.99,
+                        r"${\to}$ " + "%s" % str(var_names[j]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="center",
+                        verticalalignment="top",
+                        transform=trans,
+                    )
+
+                self.axes_dict[(i, j)].axis["right"].set_visible(False)
+                self.axes_dict[(i, j)].axis["top"].set_visible(False)
+
+                if j != 0:
+                    self.axes_dict[(i, j)].get_yaxis().set_ticklabels([])
+                if i != N - 1:
+                    self.axes_dict[(i, j)].get_xaxis().set_ticklabels([])
+
+                if plot_gridlines:
+                    self.axes_dict[(i, j)].grid(
+                        True,
+                        which="major",
+                        color="black",
+                        linestyle="dotted",
+                        dashes=(1, 1),
+                        linewidth=0.05,
+                        zorder=-5,
+                    )
+                self.axes_dict[(i, j)].tick_params(axis='both', which='major', labelsize=tick_label_size)
+
+                plot_index += 1
+
+    def add_scatterplot(
+        self,
+        dataframe,
+        matrix_lags=None,
+        color="black",
+        label=None,
+        marker=".",
+        markersize=5,
+        alpha=.2,
+        selected_dataset=0,
+    ):
+        """Add scatter plot.
+
+        Parameters
+        ----------
+        dataframe : data object
+            Tigramite dataframe object. It must have the attributes dataframe.values
+            yielding a numpy array of shape (observations T, variables N) and
+            optionally a mask of the same shape and a missing values flag.
+        matrix_lags : array
+            Lags to use in scatter plots. Either None or of shape (N, N). Then the
+            entry matrix_lags[i, j] = tau will depict the scatter plot of 
+            time series (i, -tau) vs (j, 0). If None, tau = 0 for i != j and for i = j
+            tau = 1. 
+        color : str, optional (default: 'black')
+            Line color.
+        label : str
+            Test statistic label.
+        marker : matplotlib marker symbol, optional (default: '.')
+            Marker.
+        markersize : int, optional (default: 5)
+            Marker size.
+        alpha : float, optional (default: 1.)
+            Opacity.
+        selected_dataset : int, optional (default: 0)
+            In case of multiple datasets in dataframe, plot this one.
+        """
+
+        if matrix_lags is not None and np.any(matrix_lags < 0):
+            raise ValueError("matrix_lags must be non-negative!")
+
+        data = dataframe.values[selected_dataset]
+        if dataframe.mask is not None:
+            mask = dataframe.mask[selected_dataset]
+
+        T, dim = data.shape
+
+        if label is not None:
+            self.labels.append((label, color, marker, markersize, alpha))
+
+        for ij in list(self.axes_dict):
+            i = ij[0]
+            j = ij[1]
+            if matrix_lags is None:
+                if i == j:
+                    lag = 1
+                else:
+                    lag = 0
+            else:
+                lag = matrix_lags[i,j]
+            x = np.copy(data[:T-lag, i])
+            y = np.copy(data[lag:, j])
+            if dataframe.mask is not None:
+                x[mask[:T-lag, i]==1] = np.nan
+                y[mask[lag:, j]==1] = np.nan
+
+            # print(i, j, lag, x.shape, y.shape)
+            self.axes_dict[(i, j)].scatter(
+                y, x,    # NEW: inverted to match rows and columns!
+                color=color,
+                marker=marker,
+                s=markersize,
+                alpha=alpha,
+                clip_on=False,
+                label=r"$\tau{=}%d$" %lag,
+            )
+            # self.axes_dict[(i, j)].text(0., 1., r"$\tau{=}%d$" %lag, 
+            #     fontsize=self.legend_fontsize,
+            #     ha='left', va='top',
+            #     transform=self.axes_dict[(i, j)].transAxes)
+
+
+    def adjustfig(self, name=None):
+        """Adjust matrix figure.
+
+        Parameters
+        ----------
+        name : str, optional (default: None)
+            File name. If None, figure is shown in window.
+        """
+
+        # Trick to plot legends
+        colors = []
+        for item in self.labels:
+            colors.append(item[1])
+        for ij in list(self.axes_dict):
+            i = ij[0]
+            j = ij[1]
+
+            leg = self.axes_dict[(i, j)].legend(
+                # loc="upper left",
+                ncol=1,
+                # bbox_to_anchor=(1.05, 0.0, 0.1, 1.0),
+                # borderaxespad=0,
+                fontsize=self.legend_fontsize-2,
+                labelcolor=colors,
+                ).draw_frame(False)
+
+        if len(self.labels) > 0:
+            axlegend = self.fig.add_subplot(111, frameon=False)
+            axlegend.spines["left"].set_color("none")
+            axlegend.spines["right"].set_color("none")
+            axlegend.spines["bottom"].set_color("none")
+            axlegend.spines["top"].set_color("none")
+            axlegend.set_xticks([])
+            axlegend.set_yticks([])
+
+            # self.labels.append((label, color, marker, markersize, alpha))
+            for item in self.labels:
+                label = item[0]
+                color = item[1]
+                marker = item[2]
+                markersize = item[3]
+                alpha = item[4]
+
+                axlegend.plot(
+                    [],
+                    [],
+                    linestyle="",
+                    color=color,
+                    marker=marker,
+                    markersize=markersize,
+                    label=label,
+                    alpha=alpha,
+                )
+            axlegend.legend(
+                loc="upper left",
+                ncol=1,
+                bbox_to_anchor=(1.05, 0.0, 0.1, 1.0),
+                borderaxespad=0,
+                fontsize=self.legend_fontsize,
+            ).draw_frame(False)
+
+            self.fig.subplots_adjust(
+                bottom=0.05,
+                left=self.label_space_left,
+                right=1.0 - self.legend_width,
+                top=1.0 - self.label_space_top,
+                hspace=0.5,
+                wspace=0.35,
+            )
+
+        else:
+            self.fig.subplots_adjust(
+                left=self.label_space_left,
+                bottom=0.05,
+                right=0.95,
+                top=1.0 - self.label_space_top,
+                hspace=0.35,
+                wspace=0.35,
+            )
+
+        if name is not None:
+            self.fig.savefig(name)
+        else:
+            pyplot.show()
+
+
+def plot_densityplots(dataframe,
+                      name=None,
+                      setup_args={},
+                      add_densityplot_args={},
+                      selected_dataset=0,
+                      show_marginal_densities_on_diagonal=True):
+    """Wrapper helper function to plot density plots.
+    Sets up the matrix object and plots the density plots, see parameters in
+    setup_density_matrix and add_densityplot.
+
+    The diagonal shows the marginal densities. 
+
+    Requires seaborn.
+
+    Parameters
+    ----------
+    dataframe : data object
+        Tigramite dataframe object. It must have the attributes dataframe.values
+        yielding a numpy array of shape (observations T, variables N) and
+        optionally a mask of the same shape and a missing values flag.
+    name : str, optional (default: None)
+        File name. If None, figure is shown in window.
+    setup_args : dict
+        Arguments for setting up the density plot matrix, see doc of
+        setup_density_matrix.
+    add_densityplot_args : dict
+        Arguments for adding a density plot matrix.
+    selected_dataset : int, optional (default: 0)
+        In case of multiple datasets in dataframe, plot this one.
+    show_marginal_densities_on_diagonal : bool, optional (default: True)
+        Flag to show marginal densities on the diagonal of the density plots
+
+    Returns
+    -------
+    matrix : object
+        Further density plots can be overlaid using the
+        matrix.add_densityplot function.
+    """
+
+    N = dataframe.N
+
+    matrix = setup_density_matrix(N=N, var_names=dataframe.var_names, **setup_args)
+    matrix.add_densityplot(dataframe=dataframe, selected_dataset=selected_dataset,
+                           show_marginal_densities_on_diagonal=show_marginal_densities_on_diagonal, **add_densityplot_args)
+    matrix.adjustfig(name=name)
+
+
+    return matrix
+
+
+class setup_density_matrix:
+    """Create matrix of density plot panels.
+    Class to setup figure object. The function add_densityplot allows to plot
+    density plots of variables in the dataframe. 
+
+    Further density plots can be overlaid using the matrix.add_densityplot 
+    function.
+
+    Parameters
+    ----------
+    N : int
+        Number of variables
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    figsize : tuple of floats, optional (default: None)
+        Figure size if new figure is created. If None, default pyplot figsize
+        is used.
+    label_space_left : float, optional (default: 0.1)
+        Fraction of horizontal figure space to allocate left of plot for labels.
+    label_space_top : float, optional (default: 0.05)
+        Fraction of vertical figure space to allocate top of plot for labels.
+    legend_width : float, optional (default: 0.15)
+        Fraction of horizontal figure space to allocate right of plot for
+        legend.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    plot_gridlines : bool, optional (default: False)
+        Whether to show a grid.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of variable labels.
+    """
+
+    def __init__(
+        self,
+        N,
+        var_names=None,
+        figsize=None,
+        label_space_left=0.15,
+        label_space_top=0.05,
+        legend_width=0.15,
+        legend_fontsize=10,
+        tick_label_size=6,
+        plot_gridlines=False,
+        label_fontsize=10,
+    ):
+
+        self.labels = []
+
+        self.legend_width = legend_width
+        self.legend_fontsize = legend_fontsize
+
+        self.label_space_left = label_space_left
+        self.label_space_top = label_space_top
+        self.label_fontsize = label_fontsize
+
+        self.fig = pyplot.figure(figsize=figsize)
+
+        self.axes_dict = {}
+
+        if var_names is None:
+            var_names = range(N)
+
+        plot_index = 1
+        for i in range(N):
+            for j in range(N):
+                self.axes_dict[(i, j)] = self.fig.add_subplot(N, N, plot_index)
+                # Plot process labels
+                if j == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.fig.transFigure, self.axes_dict[(i, j)].transAxes
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.01,
+                        0.5,
+                        "%s" % str(var_names[i]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="left",
+                        verticalalignment="center",
+                        transform=trans,
+                    )
+                if i == 0:
+                    trans = transforms.blended_transform_factory(
+                        self.axes_dict[(i, j)].transAxes, self.fig.transFigure
+                    )
+                    self.axes_dict[(i, j)].text(
+                        0.5,
+                        0.99,
+                        r"${\to}$ " + "%s" % str(var_names[j]),
+                        fontsize=label_fontsize,
+                        horizontalalignment="center",
+                        verticalalignment="top",
+                        transform=trans,
+                    )
+
+                # _make_nice_axes(self.axes_dict[(i, j)], where=["bottom"], skip=(1, 1)             )
+                # self.axes_dict[(i, j)].axis["right"].set_visible(False)
+                # self.axes_dict[(i, j)].axis["top"].set_visible(False)
+                if i == j:
+                    # self.axes_dict[(i, j)].axis["left"].set_visible(False)
+                    _make_nice_axes(self.axes_dict[(i, j)], where=["bottom"], skip=(1, 1))
+                else:
+                    _make_nice_axes(self.axes_dict[(i, j)], where=["left", "bottom"], skip=(1, 1))
+                # if j != 0:
+                #     self.axes_dict[(i, j)].get_yaxis().set_ticklabels([])
+                # if i != N - 1:
+                #     self.axes_dict[(i, j)].get_xaxis().set_ticklabels([])
+
+                if plot_gridlines:
+                    self.axes_dict[(i, j)].grid(
+                        True,
+                        which="major",
+                        color="black",
+                        linestyle="dotted",
+                        dashes=(1, 1),
+                        linewidth=0.05,
+                        zorder=-5,
+                    )
+                self.axes_dict[(i, j)].tick_params(axis='both', which='major', labelsize=tick_label_size)
+                plot_index += 1
+
+    def add_densityplot(
+        self,
+        dataframe,
+        matrix_lags=None,
+        label=None,
+        label_color='black',
+        snskdeplot_args = {'cmap':'Greys'},
+        snskdeplot_diagonal_args = {},
+        selected_dataset=0,
+        show_marginal_densities_on_diagonal=True
+    ):
+        """Add density function plot.
+
+        Parameters
+        ----------
+        dataframe : data object
+            Tigramite dataframe object. It must have the attributes dataframe.values
+            yielding a numpy array of shape (observations T, variables N) and
+            optionally a mask of the same shape and a missing values flag.
+        matrix_lags : array
+            Lags to use in scatter plots. Either None or non-neg array of shape (N, N). Then the
+            entry matrix_lags[i, j] = tau will depict the scatter plot of 
+            time series (i, -tau) vs (j, 0). If None, tau = 0 for i != j and for i = j
+            tau = 1. 
+        snskdeplot_args : dict
+            Optional parameters to pass to sns.kdeplot() for i != j for off-diagonal plots.
+        snskdeplot_diagonal_args : dict
+            Optional parameters to pass to sns.kdeplot() for i == j on diagonal.
+        label : string
+            Label of this plot.
+        label_color : string
+            Color of line created just for legend.
+        selected_dataset : int, optional (default: 0)
+            In case of multiple datasets in dataframe, plot this one.
+        show_marginal_densities_on_diagonal : bool, optional (default: True)
+            Flag to show marginal densities on the diagonal of the density plots
+        """
+
+        # Use seaborn for this one
+        import seaborn as sns
+
+        # set seaborn style
+        sns.set_style("white")
+
+        self.matrix_lags = matrix_lags
+
+        if matrix_lags is not None and np.any(matrix_lags < 0):
+            raise ValueError("matrix_lags must be non-negative!")
+
+        data = dataframe.values[selected_dataset]
+        if dataframe.mask is not None:
+            mask = dataframe.mask[selected_dataset]
+
+        T, dim = data.shape
+
+        # if label is not None:
+        self.labels.append((label, label_color))
+
+        for ij in list(self.axes_dict):
+            i = ij[0]
+            j = ij[1]
+            ax = self.axes_dict[(i, j)]
+            if (matrix_lags is None):
+                if i == j:
+                    lag = 1
+                else:
+                    lag = 0
+            else:
+                lag = matrix_lags[i,j]
+            x = np.copy(data[:T-lag, i])
+            y = np.copy(data[lag:, j])
+            # Data is set to NaN in dataframe init already
+            # if dataframe.missing_flag is not None:
+            #     x[x==dataframe.missing_flag] = np.nan
+            #     y[y==dataframe.missing_flag] = np.nan
+            if dataframe.mask is not None:
+                x[mask[:T-lag, i]==1] = np.nan
+                y[mask[lag:, j]==1] = np.nan
+
+            if i == j and show_marginal_densities_on_diagonal:
+                sns.kdeplot(x,
+                    color = label_color,
+                    # label=r"$\tau{=}%d$" %lag,
+                    **snskdeplot_diagonal_args,
+                    ax = ax)
+                ax.set_ylabel("")
+                # ax.yaxis.set_ticks_position("none")
+                # ax.yaxis.set_ticklabels([])
+            else:
+                sns.kdeplot(x=y, y=x,        # NEW: inverted to match rows/columns
+                    #label=r"$\tau{=}%d$" %lag,
+                    **snskdeplot_args,
+                    # fill=True,
+                    # alpha=0.3,
+                    ax = ax)
+
+    def adjustfig(self, name=None, show_labels=True):
+        """Adjust matrix figure.
+
+        Parameters
+        ----------
+        name : str, optional (default: None)
+            File name. If None, figure is shown in window.
+        """
+
+        # Trick to plot legends
+        # colors = []
+        # for item in self.labels:
+        #     colors.append(item[1])
+        for ij in list(self.axes_dict):
+            i = ij[0]
+            j = ij[1]
+            if self.matrix_lags is None:
+                lag = 0
+            else:
+                lag = self.matrix_lags[i,j]
+            if i != j:
+                colors = []
+                for item in self.labels:
+                    color = item[1]
+                    colors.append(color)
+                    if show_labels:
+                        self.axes_dict[(i, j)].plot(
+                            [],
+                            [],
+                            linestyle="",
+                            color=color,
+                            label=r"$\tau{=}%d$" %lag,
+                    )
+                # print('here')
+                leg = self.axes_dict[(i, j)].legend(
+                    # loc="best",
+                    ncol=1,
+                    # bbox_to_anchor=(1.05, 0.0, 0.1, 1.0),
+                    # borderaxespad=0,
+                    fontsize=self.legend_fontsize-2,
+                    labelcolor=colors,
+                    ).draw_frame(False)
+
+            # if i == j:
+            #     # self.axes_dict[(i, j)].axis["left"].set_visible(False)
+            #     _make_nice_axes(ax=self.axes_dict[(i, j)], where=["bottom"], skip=(1, 1))
+            # else:
+            # _make_nice_axes(ax=self.axes_dict[(i, j)], where=["left", "bottom"], skip=(1, 1))
+
+        if show_labels and len(self.labels) > 1:
+            axlegend = self.fig.add_subplot(111, frameon=False)
+            axlegend.spines["left"].set_color("none")
+            axlegend.spines["right"].set_color("none")
+            axlegend.spines["bottom"].set_color("none")
+            axlegend.spines["top"].set_color("none")
+            axlegend.set_xticks([])
+            axlegend.set_yticks([])
+
+            # self.labels.append((label, color, marker, markersize, alpha))
+            for item in self.labels:
+                label = item[0]
+                color = item[1]
+
+                axlegend.plot(
+                    [],
+                    [],
+                    linestyle="-",
+                    color=color,
+                    label=label,
+                )
+            axlegend.legend(
+                loc="upper left",
+                ncol=1,
+                bbox_to_anchor=(1.05, 0.0, 0.1, 1.0),
+                borderaxespad=0,
+                fontsize=self.legend_fontsize,
+            ).draw_frame(False)
+
+            self.fig.subplots_adjust(
+                bottom=0.08,
+                left=self.label_space_left,
+                right=1.0 - self.legend_width,
+                top=1.0 - self.label_space_top,
+                hspace=0.5,
+                wspace=0.35,
+            )
+
+        else:
+            self.fig.subplots_adjust(
+                left=self.label_space_left,
+                bottom=0.08,
+                right=0.95,
+                top=1.0 - self.label_space_top,
+                hspace=0.35,
+                wspace=0.35,
+            )
+
+        if name is not None:
+            self.fig.savefig(name)
+        else:
+            pyplot.show()
+
+def _draw_network_with_curved_edges(
+        fig,
+        ax,
+        G,
+        pos,
+        node_rings,
+        node_labels,
+        node_label_size=10,
+        node_alpha=1.0,
+        standard_size=100,
+        node_aspect=None,
+        standard_cmap="OrRd",
+        standard_color_links='black',
+        standard_color_nodes='lightgrey',
+        log_sizes=False,
+        cmap_links="YlOrRd",
+        # cmap_links_edges="YlOrRd",
+        links_vmin=0.0,
+        links_vmax=1.0,
+        links_edges_vmin=0.0,
+        links_edges_vmax=1.0,
+        links_ticks=0.2,
+        links_edges_ticks=0.2,
+        link_label_fontsize=8,
+        arrowstyle="->, head_width=0.4, head_length=1",
+        arrowhead_size=3.0,
+        curved_radius=0.2,
+        label_fontsize=4,
+        label_fraction=0.5,
+        link_colorbar_label="link",
+        tick_label_size=6,
+        # link_edge_colorbar_label='link_edge',
+        inner_edge_curved=False,
+        inner_edge_style="solid",
+        # network_lower_bound=0.2,
+        network_left_bound=None,
+        show_colorbar=True,
+        special_nodes=None,
+        autodep_sig_lags=None,
+        show_autodependency_lags=False,
+        transform='data',
+        node_classification=None,
+        max_lag=0,
+        special_links=None,
+):
+    """Function to draw a network from networkx graph instance.
+    Various attributes are used to specify the graph's properties.
+    This function is just a beta-template for now that can be further
+    customized.
+    """
+
+    if transform == 'data':
+        transform = ax.transData
+
+    from matplotlib.patches import FancyArrowPatch, Circle, Ellipse
+
+    ax.spines["left"].set_color("none")
+    ax.spines["right"].set_color("none")
+    ax.spines["bottom"].set_color("none")
+    ax.spines["top"].set_color("none")
+    ax.set_xticks([])
+    ax.set_yticks([])
+
+    N = len(G)
+
+    # This fixes a positioning bug in matplotlib.
+    ax.scatter(0, 0, zorder=-10, alpha=0)
+
+    def draw_edge(
+        ax,
+        u,
+        v,
+        d,
+        seen,
+        arrowstyle= "Simple, head_width=2, head_length=2, tail_width=1",
+        outer_edge=True,
+        cycle_edges_call_count=0
+    ):
+
+        # avoiding attribute error raised by changes in networkx
+        if hasattr(G, "node"):
+            # works with networkx 1.10
+            n1 = G.node[u]["patch"]
+            n2 = G.node[v]["patch"]
+        else:
+            # works with networkx 2.4
+            n1 = G.nodes[u]["patch"]
+            n2 = G.nodes[v]["patch"]
+
+        # print("+++++++++++++++++++++++==cmap_links ", cmap_links)
+        if outer_edge:
+
+            rad = -1.0 * curved_radius
+            if cmap_links is not None:
+                facecolor = data_to_rgb_links.to_rgba(d["outer_edge_color"])
+            else:
+                if d["outer_edge_color"] is not None:
+                    facecolor = d["outer_edge_color"]
+                else:
+                    facecolor = standard_color_links
+
+            width = d["outer_edge_width"]
+            alpha = d["outer_edge_alpha"]
+            if (u, v) in seen:
+                rad = seen.get((u, v))
+                rad = (rad + np.sign(rad) * 0.1) * -1.0
+            arrowstyle = arrowstyle
+            # link_edge = d['outer_edge_edge']
+            linestyle = 'solid' # d.get("outer_edge_style")
+
+            if cycle_edges_call_count==0:
+
+                if d.get("outer_edge_attribute", None) == "spurious":
+                    facecolor = "grey"
+
+                if d.get("outer_edge_type") in ["<-o", "<--", "<-x", "<-+"]:
+                    n1, n2 = n2, n1
+
+                if d.get("outer_edge_type") in [
+                    "o-o",
+                    "o--",
+                    "--o",
+                    "---",
+                    "x-x",
+                    "x--",
+                    "--x",
+                    "o-x",
+                    "x-o",
+                    # "+->",
+                    # "<-+",
+                ]:
+                    arrowstyle = "-"
+                    # linewidth = width*factor
+                elif d.get("outer_edge_type") == "<->":
+                    # arrowstyle = "<->, head_width=0.4, head_length=1"
+                    arrowstyle = "Simple, head_width=2, head_length=2, tail_width=1" #%float(width/20.)
+                elif d.get("outer_edge_type") in ["o->", "-->", "<-o", "<--", "<-x", "x->", "+->", "<-+"]:
+                    # arrowstyle = "->, head_width=0.4, head_length=1"
+                    # arrowstyle = "->, head_width=0.4, head_length=1, width=10"
+                    arrowstyle = "Simple, head_width=2, head_length=2, tail_width=1" #%float(width/20.)
+                else:
+                    arrowstyle = "Simple, head_width=2, head_length=2, tail_width=1" #%float(width/20.)
+                    # raise ValueError("edge type %s not valid." %d.get("outer_edge_type"))
+
+                if special_links is not None and special_links.vanishing_link(u, v):
+                    facecolor = special_links.get_color(u, v)
+                    # draw_edge(ax, u, v, d, seen, arrowstyle, outer_edge,          # color edge plus forground edge (eg corr-color)
+                    #           cycle_edges_call_count=cycle_edges_call_count + 1)
+                    arrowstyle = "Simple, head_width=1.9, head_length=1.8, tail_width=0.8" #%float(width/20.)
+
+            else: # cycle_edges_call_count > 1  # Added: Draw Vanishing edge
+                facecolor = special_links.get_color(u, v)
+                arrowstyle = "Simple, head_width=2.5, head_length=2.2, tail_width=1.5" #%float(width/20.)
+
+        else: # if inner edge:
+            rad = -1.0 * inner_edge_curved * curved_radius
+            if cmap_links is not None:
+                facecolor = data_to_rgb_links.to_rgba(d["inner_edge_color"])
+            else:
+                if d["inner_edge_color"] is not None:
+                    facecolor = d["inner_edge_color"]
+                else:
+                    # print("HERE")
+                    facecolor = standard_color_links
+
+            width = d["inner_edge_width"]
+            alpha = d["inner_edge_alpha"]
+
+            if d.get("inner_edge_attribute", None) == "spurious":
+                facecolor = "grey"
+            # print(d.get("inner_edge_type"))
+            if d.get("inner_edge_type") in ["<-o", "<--", "<-x", "<-+"]:
+                n1, n2 = n2, n1
+
+            def get_arrow_style(edge_type: str, scale: float=1.0) -> str:
+                if edge_type in [
+                    "o-o",
+                    "o--",
+                    "--o",
+                    "---",
+                    "x-x",
+                    "x--",
+                    "--x",
+                    "o-x",
+                    "x-o",
+                ]:
+                    # return "-"
+                    return f"simple, tail_width={scale * 1.0}"
+                elif edge_type == "<->":
+                    # arrowstyle = "<->, head_width=0.4, head_length=1"
+                    return f"Simple, head_width={scale * 2.0}, head_length={scale * 2.0}, tail_width={scale * 1.0}" #%float(width/20.)
+                elif edge_type in ["o->", "-->", "<-o", "<--", "<-x", "x->", "+->", "<-+"]:
+                    # arrowstyle = "->, head_width=0.4, head_length=1"
+                    return f"Simple, head_width={scale * 2.0}, head_length={scale * 2.0}, tail_width={scale * 1.0}" #%float(width/20.)
+                elif edge_type == "<O>": # Added: Draw Edge-Flip
+                    # arrowstyle = "<->, head_width=0.4, head_length=1"
+                    assert False
+                    if cycle_edges_call_count < 3:
+                        draw_edge(ax, v, u, d, seen, arrowstyle, outer_edge, cycle_edges_call_count=cycle_edges_call_count+1)
+
+                    rad = -2.0 * curved_radius
+                    if cycle_edges_call_count < 2: # drawn in inverse order (draw executes synchronously ...)
+                        facecolor = data_to_rgb_links.to_rgba(d["inner_edge_color"])
+                        arrowstyle = "Simple, head_width=1.9, head_length=2.0, tail_width=0.7" #%float(width/20.)
+                    else:
+                        facecolor = special_links.get_color(u, v)
+                        arrowstyle = "Simple, head_width=2.5, head_length=2.2, tail_width=1.5" #%float(width/20.)
+                else:
+                    return f"Simple, head_width={scale * 2.0}, head_length={scale * 2.0}, tail_width={scale * 1.0}" #%float(width/20.)
+
+                
+            if cycle_edges_call_count==0:
+                
+                # added:
+                arrowstyle = None
+                if special_links is not None and special_links.vanishing_link(u, v):
+                    arrowstyle = get_arrow_style( d.get("inner_edge_type"), scale=0.8 )
+                    
+                    facecolor = special_links.get_color(u, v)
+                    # draw_edge(ax, u, v, d, seen, arrowstyle, outer_edge,  # color edge plus forground edge (eg corr-color)
+                    #             cycle_edges_call_count=cycle_edges_call_count + 1)
+                    
+                    # eg for '°-°' for arrowstyle = "-" ...
+                else:                    
+                    arrowstyle = get_arrow_style( d.get("inner_edge_type") )
+
+                #     raise ValueError("edge type %s not valid." %d.get("inner_edge_type"))
+
+                linestyle = 'solid' #d.get("inner_edge_style")
+            
+            else: # cycle_edges_call_count > 1  # Added: Draw Vanishing edge
+                facecolor = special_links.get_color(u, v)
+                arrowstyle = get_arrow_style( d.get("inner_edge_type"), scale=1.3 )
+                
+                linestyle = 'solid' #d.get("inner_edge_style")
+
+        coor1 = n1.center
+        coor2 = n2.center
+
+        marker_size = width ** 2
+        figuresize = fig.get_size_inches()
+
+        # print("COLOR ", facecolor)
+        # print(u, v, outer_edge, "outer ", d.get("outer_edge_type"),  "inner ",  d.get("inner_edge_type"), width, arrowstyle, linestyle)
+
+        if ((outer_edge is True and d.get("outer_edge_type") == "<->")
+           or (outer_edge is False and d.get("inner_edge_type") == "<->")):
+            e_p = FancyArrowPatch(
+                coor1,
+                coor2,
+                arrowstyle=arrowstyle,
+                connectionstyle=f"arc3,rad={rad}",
+                mutation_scale=1*width,
+                lw=0., #width / 2.,
+                aa=True,
+                alpha=alpha,
+                linestyle=linestyle,
+                color=facecolor,
+                clip_on=False,
+                patchA=n1,
+                patchB=n2,
+                shrinkA=7,
+                shrinkB=0,
+                zorder=-1,
+                capstyle="butt",
+                transform=transform,
+            )
+            ax.add_artist(e_p)
+
+            e_p_back = FancyArrowPatch(
+              coor2,
+              coor1,
+              arrowstyle=arrowstyle,
+              connectionstyle=f"arc3,rad={-rad}",
+              mutation_scale=1*width,
+              lw=0., #width / 2.,
+              aa=True,
+              alpha=alpha,
+              linestyle=linestyle,
+              color=facecolor,
+              clip_on=False,
+              patchA=n2,
+              patchB=n1,
+              shrinkA=7,
+              shrinkB=0,
+              zorder=-1,
+              capstyle="butt",
+              transform=transform,
+            )
+            ax.add_artist(e_p_back)
+
+        else:
+            if arrowstyle == '-':
+                lw = 1*width
+            else:
+                lw = 0.
+            # e_p = FancyArrowPatch(
+            #     coor1,
+            #     coor2,
+            #     arrowstyle=arrowstyle,
+            #     connectionstyle=f"arc3,rad={rad}",
+            #     mutation_scale=np.sqrt(width)*2*1.1,
+            #     lw=lw*1.1, #width / 2.,
+            #     aa=True,
+            #     alpha=alpha,
+            #     linestyle=linestyle,
+            #     color='white',
+            #     clip_on=False,
+            #     patchA=n1,
+            #     patchB=n2,
+            #     shrinkA=0,
+            #     shrinkB=0,
+            #     zorder=-1,
+            #     capstyle="butt",
+            # )
+            # ax.add_artist(e_p)
+            e_p = FancyArrowPatch(
+                coor1,
+                coor2,
+                arrowstyle=arrowstyle,
+                connectionstyle=f"arc3,rad={rad}",
+                mutation_scale=1*width,
+                lw=lw, #width / 2.,
+                aa=True,
+                alpha=alpha,
+                linestyle=linestyle,
+                color=facecolor,
+                clip_on=False,
+                patchA=n1,
+                patchB=n2,
+                shrinkA=0,
+                shrinkB=0,
+                # zorder=-1,
+                capstyle="butt",
+                transform=transform,
+            )
+            ax.add_artist(e_p)
+
+        e_p_marker = FancyArrowPatch(
+                coor1,
+                coor2,
+                arrowstyle='-',
+                connectionstyle=f"arc3,rad={rad}",
+                mutation_scale=1*width,
+                lw=0., #width / 2.,
+                aa=True,
+                alpha=0.,
+                linestyle=linestyle,
+                color=facecolor,
+                clip_on=False,
+                patchA=n1,
+                patchB=n2,
+                shrinkA=0,
+                shrinkB=0,
+                zorder=-10,
+                capstyle="butt",
+                transform=transform,
+        )
+        ax.add_artist(e_p_marker)
+
+        # marker_path = e_p_marker.get_path()
+        vertices = e_p_marker.get_path().vertices.copy()
+        # vertices = e_p_marker.get_verts()
+        # vertices = e_p_marker.get_path().to_polygons(transform=None)[0]
+        # print(vertices.shape)
+        m, n = vertices.shape
+
+        # print(vertices)
+        start = vertices[0]
+        end = vertices[-1]
+
+        # This must be added to avoid rescaling of the plot, when no 'o'
+        # or 'x' is added to the graph.
+        ax.scatter(*start, zorder=-10, alpha=0, transform=transform,)
+
+        if outer_edge:
+            if d.get("outer_edge_type") in ["o->", "o--"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("outer_edge_type") == "<-o":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "--o":
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") in ["x--", "x->"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("outer_edge_type") in ["+--", "+->"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="P",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("outer_edge_type") == "<-x":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "<-+":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="P",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "--x":
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "o-o":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "x-x":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "o-x":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("outer_edge_type") == "x-o":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+
+        else:
+            if d.get("inner_edge_type") in ["o->", "o--"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("inner_edge_type") == "<-o":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "--o":
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") in ["x--", "x->"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("inner_edge_type") in ["+--", "+->"]:
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="P",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+            elif d.get("inner_edge_type") == "<-x":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "<-+":
+                circle_marker_end = ax.scatter(
+                    *start,
+                    marker="P",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "--x":
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "o-o":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "x-x":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "o-x":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+            elif d.get("inner_edge_type") == "x-o":
+                circle_marker_start = ax.scatter(
+                    *start,
+                    marker="X",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_start)
+                circle_marker_end = ax.scatter(
+                    *end,
+                    marker="o",
+                    s=marker_size,
+                    facecolor="w",
+                    edgecolor=facecolor,
+                    zorder=1,
+                    transform=transform,
+                )
+                ax.add_collection(circle_marker_end)
+
+
+
+        if d["label"] is not None and outer_edge:
+            def closest_node(node, nodes):
+                nodes = np.asarray(nodes)
+                node = node.reshape(1, 2)
+                dist_2 = np.sum((nodes - node)**2, axis=1)
+                return np.argmin(dist_2)
+
+            # Attach labels of lags
+            # trans = None  # patch.get_transform()
+            # path = e_p.get_path()
+            vertices = e_p_marker.get_path().vertices.copy()
+            verts = e_p.get_path().to_polygons(transform=None)[0]
+            # print(verts)
+            # print(verts.shape)
+            # print(vertices.shape)
+            # for num, vert in enumerate(verts):
+            #     ax.text(vert[0], vert[1], str(num), 
+            #         transform=transform,)
+            # ax.scatter(verts[:,0], verts[:,1])
+            # mid_point = np.array([(start[0] + end[0])/2., (start[1] + end[1])/2.])
+            # print(start, end, mid_point)
+            # ax.scatter(mid_point[0], mid_point[1], marker='x', 
+            #     s=100, zorder=10, transform=transform,)
+            closest_node = closest_node(vertices[int(len(vertices)/2.),:], verts)
+            # print(closest_node, verts[closest_node])
+            # ax.scatter(verts[closest_node][0], verts[closest_node][1], marker='x')
+
+            if len(vertices) > 2:
+                # label_vert = vertices[int(len(vertices)/2.),:] #verts[1, :]
+                label_vert = verts[closest_node] #verts[1, :]
+                l = d["label"]
+                string = str(l)
+                txt = ax.text(
+                    label_vert[0],
+                    label_vert[1],
+                    string,
+                    fontsize=link_label_fontsize,
+                    verticalalignment="center",
+                    horizontalalignment="center",
+                    color="w",
+                    zorder=1,
+                    transform=transform,
+                )
+                txt.set_path_effects(
+                    [PathEffects.withStroke(linewidth=2, foreground="k")]
+                )
+
+        return rad
+
+    # Collect all edge weights to get color scale
+    all_links_weights = []
+    all_links_edge_weights = []
+    for (u, v, d) in G.edges(data=True):
+        if u != v:
+            if d["outer_edge"] and d["outer_edge_color"] is not None:
+                all_links_weights.append(d["outer_edge_color"])
+            if d["inner_edge"] and d["inner_edge_color"] is not None:
+                all_links_weights.append(d["inner_edge_color"])
+
+    if cmap_links is not None and len(all_links_weights) > 0:
+        if links_vmin is None:
+            links_vmin = np.array(all_links_weights).min()
+        if links_vmax is None:
+            links_vmax = np.array(all_links_weights).max()
+        data_to_rgb_links = pyplot.cm.ScalarMappable(
+            norm=None, cmap=pyplot.get_cmap(cmap_links)
+        )
+        data_to_rgb_links.set_array(np.array(all_links_weights))
+        data_to_rgb_links.set_clim(vmin=links_vmin, vmax=links_vmax)
+        # Create colorbars for links
+
+        # setup colorbar axes.
+        if show_colorbar:
+            # cax_e = pyplot.axes(
+            #     [
+            #         0.55,
+            #         ax.get_subplotspec().get_position(ax.figure).bounds[1] + 0.02,
+            #         0.4,
+            #         0.025 + (len(all_links_edge_weights) == 0) * 0.035,
+            #     ],
+            #     frameon=False,
+            # )
+            bbox_ax = ax.get_position()
+            width = bbox_ax.xmax-bbox_ax.xmin
+            height = bbox_ax.ymax-bbox_ax.ymin
+            # print(bbox_ax.xmin, bbox_ax.xmax, bbox_ax.ymin, bbox_ax.ymax) 
+            # cax_e = fig.add_axes(
+            #     [
+            #         bbox_ax.xmax - width*0.45,
+            #         bbox_ax.ymin-0.075*height+network_lower_bound-0.15,
+            #         width*0.4,
+            #         0.075*height,   #0.025 + (len(all_links_edge_weights) == 0) * 0.035,
+            #     ],
+            #     frameon=False,
+            # )
+            cax_e = ax.inset_axes(
+                          [
+                          0.55, -0.07, 0.4, 0.07
+                    # bbox_ax.xmax - width*0.45,
+                    # bbox_ax.ymin-0.075*height+network_lower_bound-0.15,
+                    # width*0.4,
+                    # 0.075*height,   #0.025 + (len(all_links_edge_weights) == 0) * 0.035,
+                ],
+                frameon=False,)
+            # divider = make_axes_locatable(ax)
+
+            # cax_e = divider.append_axes('bottom', size='5%', pad=0.05, frameon=False,)
+
+            cb_e = pyplot.colorbar(
+                data_to_rgb_links, cax=cax_e, orientation="horizontal"
+            )
+            # try:
+            ticks_here = np.arange(
+                    _myround(links_vmin, links_ticks, "down"),
+                    _myround(links_vmax, links_ticks, "up") + links_ticks,
+                    links_ticks,
+                )
+            cb_e.set_ticks(ticks_here[(links_vmin <= ticks_here) & (ticks_here <= links_vmax)])
+            # except:
+            #     print('no ticks given')
+
+            cb_e.outline.clear()
+            cax_e.set_xlabel(
+                link_colorbar_label, labelpad=1, fontsize=label_fontsize, zorder=10
+            )
+            cax_e.tick_params(axis='both', which='major', labelsize=tick_label_size)
+
+    ##
+    # Draw nodes
+    ##
+    node_sizes = np.zeros((len(node_rings), N))
+    for ring in list(node_rings):  # iterate through to get all node sizes
+        if node_rings[ring]["sizes"] is not None:
+            node_sizes[ring] = node_rings[ring]["sizes"]
+
+        else:
+            node_sizes[ring] = standard_size
+    max_sizes = node_sizes.max(axis=1)
+    total_max_size = node_sizes.sum(axis=0).max()
+    node_sizes /= total_max_size
+    node_sizes *= standard_size
+
+    def get_aspect(ax):
+        # Total figure size
+        figW, figH = ax.get_figure().get_size_inches()
+        # print(figW, figH)
+        # Axis size on figure
+        _, _, w, h = ax.get_position().bounds
+        # Ratio of display units
+        # print(w, h)
+        disp_ratio = (figH * h) / (figW * w)
+        # Ratio of data units
+        # Negative over negative because of the order of subtraction
+        data_ratio = sub(*ax.get_ylim()) / sub(*ax.get_xlim())
+        # print(data_ratio, disp_ratio)
+        return disp_ratio / data_ratio
+
+    if node_aspect is None:
+        node_aspect = get_aspect(ax)
+
+    # start drawing the outer ring first...
+    for ring in list(node_rings)[::-1]:
+        #        print ring
+        # dictionary of rings: {0:{'sizes':(N,)-array, 'color_array':(N,)-array
+        # or None, 'cmap':string, 'vmin':float or None, 'vmax':float or None}}
+        if node_rings[ring]["color_array"] is not None:
+            color_data = node_rings[ring]["color_array"]
+            if node_rings[ring]["vmin"] is not None:
+                vmin = node_rings[ring]["vmin"]
+            else:
+                vmin = node_rings[ring]["color_array"].min()
+            if node_rings[ring]["vmax"] is not None:
+                vmax = node_rings[ring]["vmax"]
+            else:
+                vmax = node_rings[ring]["color_array"].max()
+            if node_rings[ring]["cmap"] is not None:
+                cmap = node_rings[ring]["cmap"]
+            else:
+                cmap = standard_cmap
+            data_to_rgb = pyplot.cm.ScalarMappable(
+                norm=None, cmap=pyplot.get_cmap(cmap)
+            )
+            data_to_rgb.set_array(color_data)
+            data_to_rgb.set_clim(vmin=vmin, vmax=vmax)
+            colors = [data_to_rgb.to_rgba(color_data[n]) for n in G]
+
+            if node_rings[ring]["colorbar"]:
+                # Create colorbars for nodes
+                # cax_n = pyplot.axes([.8 + ring*0.11,
+                # ax.get_subplotspec().get_position(ax.figure).bounds[1]+0.05, 0.025, 0.35], frameon=False) #
+                # setup colorbar axes.
+                # setup colorbar axes.
+                bbox_ax = ax.get_position()
+                # print(bbox_ax.xmin, bbox_ax.xmax, bbox_ax.ymin, bbox_ax.ymax) 
+                cax_n = ax.inset_axes(
+                    [
+                    0.05, -0.07, 0.4, 0.07
+                        # bbox_ax.xmin + width*0.05,
+                        # bbox_ax.ymin-0.075*height+network_lower_bound-0.15,
+                        # width*0.4,
+                        # 0.075*height,   #0.025 + (len(all_links_edge_weights) == 0) * 0.035,
+                    ],
+                    frameon=False,
+                )
+                cb_n = pyplot.colorbar(data_to_rgb, cax=cax_n, orientation="horizontal")
+                # try:
+                ticks_here = np.arange(
+                    _myround(vmin, node_rings[ring]["ticks"], "down"),
+                    _myround(vmax, node_rings[ring]["ticks"], "up")
+                    + node_rings[ring]["ticks"],
+                    node_rings[ring]["ticks"],
+                )
+                cb_n.set_ticks(ticks_here[(vmin <= ticks_here) & (ticks_here <= vmax)])
+                # except:
+                #     print ('no ticks given')
+                cb_n.outline.clear()
+                # cb_n.set_ticks()
+                cax_n.set_xlabel(
+                    node_rings[ring]["label"], labelpad=1, fontsize=label_fontsize
+                )
+                cax_n.tick_params(axis='both', which='major', labelsize=tick_label_size)
+        else:
+            colors = None
+            vmin = None
+            vmax = None
+
+        for n in G:
+            if type(node_alpha) == dict:
+                alpha = node_alpha[n]
+            else:
+                alpha = 1.0
+
+            if special_nodes is not None:
+                if n in special_nodes:
+                    color_here = special_nodes[n]
+                else:
+                    color_here = 'grey'
+            else:
+                if colors is None:
+                    color_here = standard_color_nodes
+                else:
+                    color_here = colors[n]
+
+            c = Ellipse(
+                pos[n],
+                width=node_sizes[: ring + 1].sum(axis=0)[n] * node_aspect,
+                height=node_sizes[: ring + 1].sum(axis=0)[n],
+                clip_on=False,
+                facecolor=color_here,
+                edgecolor=color_here,
+                zorder=-ring - 1 + 2,
+                transform=transform,
+            )
+
+            # else:
+            #     if special_nodes is not None and n in special_nodes:
+            #         color_here = special_nodes[n]
+            #     else:
+            #         color_here = colors[n]
+            #     c = Ellipse(
+            #         pos[n],
+            #         width=node_sizes[: ring + 1].sum(axis=0)[n] * node_aspect,
+            #         height=node_sizes[: ring + 1].sum(axis=0)[n],
+            #         clip_on=False,
+            #         facecolor=colors[n],
+            #         edgecolor=colors[n],
+            #         zorder=-ring - 1,
+            #     )
+
+            ax.add_patch(c)
+
+            if node_classification is not None and node_classification[n] in ["space_context_last", "space_dummy_last", "time_dummy_last"]:
+                node_height = node_sizes[: ring + 1].sum(axis=0)[n]
+                node_width_difference_to_height = node_height * (1 - node_aspect)
+
+                c_wide = mpatches.FancyBboxPatch((pos[n-max_lag+1][0] + node_width_difference_to_height / 2, pos[n-max_lag+1][1]),
+                                                 (pos[n][0] - pos[n-max_lag+1][0] - node_width_difference_to_height),
+                                                 0.,
+                                                 boxstyle=mpatches.BoxStyle.Round(pad=0.5 * node_height),
+                                                 facecolor=color_here,
+                                                 edgecolor=color_here,
+                                                 )
+
+                ax.add_patch(c_wide)
+
+
+            # avoiding attribute error raised by changes in networkx
+            if hasattr(G, "node"):
+                # works with networkx 1.10
+                G.node[n]["patch"] = c
+            else:
+                # works with networkx 2.4
+                G.nodes[n]["patch"] = c
+
+            if ring == 0:
+                ax.text(
+                    pos[n][0],
+                    pos[n][1],
+                    node_labels[n],
+                    fontsize=node_label_size,
+                    horizontalalignment="center",
+                    verticalalignment="center",
+                    alpha=1.0,
+                    zorder=5.,
+                    transform=transform,
+                )
+                if show_autodependency_lags:
+                    ax.text(
+                        pos[n][0],
+                        pos[n][1],
+                        autodep_sig_lags[n],
+                        fontsize=link_label_fontsize,
+                        horizontalalignment="center",
+                        verticalalignment="center",
+                        color="black",
+                        zorder=5.,
+                        transform=transform,
+                    )
+
+    # Draw edges
+    seen = {}
+    for (u, v, d) in G.edges(data=True):
+        if d.get("no_links"):
+            d["inner_edge_alpha"] = 1e-8
+            d["outer_edge_alpha"] = 1e-8
+        if u != v:
+            if d["outer_edge"]:
+                seen[(u, v)] = draw_edge(ax, u, v, d, seen, outer_edge=True)
+            if d["inner_edge"]:
+                seen[(u, v)] = draw_edge(ax, u, v, d, seen, outer_edge=False)
+
+    # if network_left_bound is not None:
+    #     network_right_bound = 0.98
+    # else:
+    #     network_right_bound = None
+    # fig.subplots_adjust(bottom=network_lower_bound, left=network_left_bound, right=network_right_bound) #, right=0.97)
+
+
+def plot_graph(
+    graph,
+    val_matrix=None,
+    var_names=None,
+    fig_ax=None,
+    figsize=None,
+    save_name=None,
+    link_colorbar_label="MCI",
+    node_colorbar_label="auto-MCI",
+    link_width=None,
+    link_attribute=None,
+    node_pos=None,
+    arrow_linewidth=8.0,
+    vmin_edges=-1,
+    vmax_edges=1.0,
+    edge_ticks=0.4,
+    cmap_edges="RdBu_r",
+    vmin_nodes=-1,
+    vmax_nodes=1.0,
+    node_ticks=0.4,
+    cmap_nodes="RdBu_r",
+    node_size=0.3,
+    node_aspect=None,
+    arrowhead_size=20,
+    curved_radius=0.2,
+    label_fontsize=10,
+    tick_label_size=6,
+    alpha=1.0,
+    node_label_size=10,
+    link_label_fontsize=10,
+    lag_array=None,
+    # network_lower_bound=0.2,
+    show_colorbar=True,
+    inner_edge_style="dashed",
+    link_matrix=None,
+    special_nodes=None,
+    show_autodependency_lags=False,
+    special_links=None,
+):
+    """Creates a network plot.
+    
+    This is still in beta. The network is defined from links in graph. Nodes
+    denote variables, straight links contemporaneous dependencies and curved
+    arrows lagged dependencies. The node color denotes the maximal absolute
+    auto-dependency and the link color the value at the lag with maximal
+    absolute cross-dependency. The link label lists the lags with significant
+    dependency in order of absolute magnitude. The network can also be
+    plotted over a map drawn before on the same axis. Then the node positions
+    can be supplied in appropriate axis coordinates via node_pos.
+
+    Parameters
+    ----------
+    graph : string or bool array-like, optional (default: None)
+        Either string matrix providing graph or bool array providing only adjacencies
+        Must be of same shape as val_matrix. 
+    val_matrix : array_like
+        Matrix of shape (N, N, tau_max+1) containing test statistic values.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    fig_ax : tuple of figure and axis object, optional (default: None)
+        Figure and axes instance. If None they are created.
+    figsize : tuple
+        Size of figure.
+    save_name : str, optional (default: None)
+        Name of figure file to save figure. If None, figure is shown in window.
+    link_colorbar_label : str, optional (default: 'MCI')
+        Test statistic label.
+    node_colorbar_label : str, optional (default: 'auto-MCI')
+        Test statistic label for auto-dependencies.
+    link_width : array-like, optional (default: None)
+        Array of val_matrix.shape specifying relative link width with maximum
+        given by arrow_linewidth. If None, all links have same width.
+    link_attribute : array-like, optional (default: None)
+        String array of val_matrix.shape specifying link attributes.
+    node_pos : dictionary, optional (default: None)
+        Dictionary of node positions in axis coordinates of form
+        node_pos = {'x':array of shape (N,), 'y':array of shape(N)}. These
+        coordinates could have been transformed before for basemap plots. You can
+        also add a key 'transform':ccrs.PlateCarree() in order to plot graphs on 
+        a map using cartopy.
+    arrow_linewidth : float, optional (default: 30)
+        Linewidth.
+    vmin_edges : float, optional (default: -1)
+        Link colorbar scale lower bound.
+    vmax_edges : float, optional (default: 1)
+        Link colorbar scale upper bound.
+    edge_ticks : float, optional (default: 0.4)
+        Link tick mark interval.
+    cmap_edges : str, optional (default: 'RdBu_r')
+        Colormap for links.
+    vmin_nodes : float, optional (default: 0)
+        Node colorbar scale lower bound.
+    vmax_nodes : float, optional (default: 1)
+        Node colorbar scale upper bound.
+    node_ticks : float, optional (default: 0.4)
+        Node tick mark interval.
+    cmap_nodes : str, optional (default: 'OrRd')
+        Colormap for links.
+    node_size : int, optional (default: 0.3)
+        Node size.
+    node_aspect : float, optional (default: None)
+        Ratio between the heigth and width of the varible nodes.
+    arrowhead_size : int, optional (default: 20)
+        Size of link arrow head. Passed on to FancyArrowPatch object.
+    curved_radius, float, optional (default: 0.2)
+        Curvature of links. Passed on to FancyArrowPatch object.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of colorbar labels.
+    alpha : float, optional (default: 1.)
+        Opacity.
+    node_label_size : int, optional (default: 10)
+        Fontsize of node labels.
+    link_label_fontsize : int, optional (default: 6)
+        Fontsize of link labels.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    lag_array : array, optional (default: None)
+        Optional specification of lags overwriting np.arange(0, tau_max+1)
+    show_colorbar : bool
+        Whether to show colorbars for links and nodes.
+    show_autodependency_lags : bool (default: False)
+        Shows significant autodependencies for a node.
+    """
+
+    if link_matrix is not None:
+        raise ValueError("link_matrix is deprecated and replaced by graph array"
+                         " which is now returned by all methods.")
+
+    if fig_ax is None:
+        fig = pyplot.figure(figsize=figsize)
+        ax = fig.add_subplot(111, frame_on=False)
+    else:
+        fig, ax = fig_ax
+
+    graph = np.copy(graph.squeeze())
+
+    if graph.ndim == 4:
+        raise ValueError("Time series graph of shape (N,N,tau_max+1,tau_max+1) cannot be represented by plot_graph,"
+                         " use plot_time_series_graph instead.")
+
+    if graph.ndim == 2:
+        # If a non-time series (N,N)-graph is given, insert a dummy dimension
+        graph = np.expand_dims(graph, axis = 2)
+
+    if val_matrix is None:
+        no_coloring = True
+        cmap_edges = None
+        cmap_nodes = None
+    else:
+        no_coloring = False
+
+    (graph, val_matrix, link_width, link_attribute) = _check_matrices(
+        graph, val_matrix, link_width, link_attribute)
+
+
+    N, N, dummy = graph.shape
+    tau_max = dummy - 1
+    max_lag = tau_max + 1
+
+    if np.count_nonzero(graph != "") == np.count_nonzero(
+        np.diagonal(graph) != ""
+    ):
+        diagonal = True
+    else:
+        diagonal = False
+
+    if np.count_nonzero(graph == "") == graph.size or diagonal:
+        graph[0, 1, 0] = "xxx"  # Workaround, will not be plotted... 
+        no_links = True
+    else:
+        no_links = False
+
+    if var_names is None:
+        var_names = range(N)
+
+    # Define graph links by absolute maximum (positive or negative like for
+    # partial correlation)
+    # val_matrix[np.abs(val_matrix) < sig_thres] = 0.
+
+    # Only draw link in one direction among contemp
+    # Remove lower triangle
+    link_matrix_upper = np.copy(graph)
+    link_matrix_upper[:, :, 0] = np.triu(link_matrix_upper[:, :, 0])
+
+    # net = _get_absmax(link_matrix != "")
+    net = np.any(link_matrix_upper != "", axis=2)
+    G = nx.DiGraph(net)
+
+    # This handels Graphs with no links.
+    # nx.draw(G, alpha=0, zorder=-10)
+
+    node_color = list(np.zeros(N))
+
+    if show_autodependency_lags:
+        autodep_sig_lags = np.full(N, None, dtype='object')
+    else:
+        autodep_sig_lags = None
+
+    # list of all strengths for color map
+    all_strengths = []
+    # Add attributes, contemporaneous and lagged links are handled separately
+    for (u, v, dic) in G.edges(data=True):
+        dic["no_links"] = no_links
+        # average lagfunc for link u --> v ANDOR u -- v
+        if tau_max > 0:
+            # argmax of absolute maximum where a link exists!
+            links = np.where(link_matrix_upper[u, v, 1:] != "")[0]
+            if len(links) > 0:
+                argmax_links = np.abs(val_matrix[u, v][1:][links]).argmax()
+                argmax = links[argmax_links] + 1
+            else:
+                argmax = 0
+        else:
+            argmax = 0
+
+        if u != v:
+            # For contemp links masking or finite samples can lead to different
+            # values for u--v and v--u
+            # Here we use the  maximum for the width and weight (=color)
+            # of the link
+            # Draw link if u--v OR v--u at lag 0 is nonzero
+            # dic['inner_edge'] = ((np.abs(val_matrix[u, v][0]) >=
+            #                       sig_thres[u, v][0]) or
+            #                      (np.abs(val_matrix[v, u][0]) >=
+            #                       sig_thres[v, u][0]))
+            dic["inner_edge"] = link_matrix_upper[u, v, 0]
+            dic["inner_edge_type"] = link_matrix_upper[u, v, 0]
+            dic["inner_edge_alpha"] = alpha
+            if no_coloring:
+                dic["inner_edge_color"] = None
+            else:
+                dic["inner_edge_color"] = val_matrix[u, v, 0]
+            # # value at argmax of average
+            # if np.abs(val_matrix[u, v][0] - val_matrix[v, u][0]) > .0001:
+            #     print("Contemporaneous I(%d; %d)=%.3f != I(%d; %d)=%.3f" % (
+            #           u, v, val_matrix[u, v][0], v, u, val_matrix[v, u][0]) +
+            #           " due to conditions, finite sample effects or "
+            #           "masking, here edge color = "
+            #           "larger (absolute) value.")
+            # dic['inner_edge_color'] = _get_absmax(
+            #     np.array([[[val_matrix[u, v][0],
+            #                    val_matrix[v, u][0]]]])).squeeze()
+
+            if link_width is None:
+                dic["inner_edge_width"] = arrow_linewidth
+            else:
+                dic["inner_edge_width"] = (
+                    link_width[u, v, 0] / link_width.max() * arrow_linewidth
+                )
+
+            if link_attribute is None:
+                dic["inner_edge_attribute"] = None
+            else:
+                dic["inner_edge_attribute"] = link_attribute[u, v, 0]
+
+            #     # fraction of nonzero values
+            dic["inner_edge_style"] = "solid"
+            # else:
+            # dic['inner_edge_style'] = link_style[
+            #         u, v, 0]
+
+            all_strengths.append(dic["inner_edge_color"])
+
+            if tau_max > 0:
+                # True if ensemble mean at lags > 0 is nonzero
+                # dic['outer_edge'] = np.any(
+                #     np.abs(val_matrix[u, v][1:]) >= sig_thres[u, v][1:])
+                dic["outer_edge"] = np.any(link_matrix_upper[u, v, 1:] != "")
+            else:
+                dic["outer_edge"] = False
+            # print(u, v, dic["outer_edge"], argmax, link_matrix_upper[u, v, :])
+
+            dic["outer_edge_type"] = link_matrix_upper[u, v, argmax]
+
+            dic["outer_edge_alpha"] = alpha
+            if link_width is None:
+                # fraction of nonzero values
+                dic["outer_edge_width"] = arrow_linewidth
+            else:
+                dic["outer_edge_width"] = (
+                    link_width[u, v, argmax] / link_width.max() * arrow_linewidth
+                )
+
+            if link_attribute is None:
+                # fraction of nonzero values
+                dic["outer_edge_attribute"] = None
+            else:
+                dic["outer_edge_attribute"] = link_attribute[u, v, argmax]
+
+            # value at argmax of average
+            if no_coloring:
+                dic["outer_edge_color"] = None
+            else:
+                dic["outer_edge_color"] = val_matrix[u, v][argmax]
+            all_strengths.append(dic["outer_edge_color"])
+
+            # Sorted list of significant lags (only if robust wrt
+            # d['min_ensemble_frac'])
+            if tau_max > 0:
+                lags = np.abs(val_matrix[u, v][1:]).argsort()[::-1] + 1
+                sig_lags = (np.where(link_matrix_upper[u, v, 1:] != "")[0] + 1).tolist()
+            else:
+                lags, sig_lags = [], []
+            if lag_array is not None:
+                dic["label"] = ",".join([str(lag_array[l]) for l in lags if l in sig_lags])  #str([str(lag_array[l]) for l in lags if l in sig_lags])[1:-1].replace(" ", "")
+            else:
+                dic["label"] = ",".join([str(l) for l in lags if l in sig_lags]) # str([str(l) for l in lags if l in sig_lags])[1:-1].replace(" ", "")
+        else:
+            # Node color is max of average autodependency
+            if no_coloring:
+                node_color[u] = None
+            else:
+                node_color[u] = val_matrix[u, v][argmax]
+
+            if show_autodependency_lags:
+                autodep_sig_lags[u] = "\n\n\n" + ",".join(str(i) for i in (np.where(link_matrix_upper[u, v, 1:] != "")[0] + 1).tolist())
+                # Lags upto tau_max
+                #autodep_lags = np.argsort(val_matrix[u, v][1:])[::-1]
+                #autodep_lags += 1
+                #autodeplags[u] = "\n\n\n" + ",".join(str(i) for i in autodep_lags.tolist())
+
+            dic["inner_edge_attribute"] = None
+            dic["outer_edge_attribute"] = None
+
+        # dic['outer_edge_edge'] = False
+        # dic['outer_edge_edgecolor'] = None
+        # dic['inner_edge_edge'] = False
+        # dic['inner_edge_edgecolor'] = None
+
+    if special_nodes is not None:
+        special_nodes_draw = {}
+        for node in special_nodes:
+            i, tau = node
+            if tau >= -tau_max:
+                special_nodes_draw[i] = special_nodes[node]
+        special_nodes = special_nodes_draw
+
+
+    # If no links are present, set value to zero
+    if len(all_strengths) == 0:
+        all_strengths = [0.0]
+
+    if node_pos is None:
+        pos = nx.circular_layout(deepcopy(G))
+    else:
+        pos = {}
+        for i in range(N):
+            pos[i] = (node_pos["x"][i], node_pos["y"][i])
+
+    if node_pos is not None and 'transform' in node_pos:
+        transform = node_pos['transform']
+    else: transform = ax.transData
+
+    if cmap_nodes is None:
+        node_color = None
+
+    node_rings = {
+        0: {
+            "sizes": None,
+            "color_array": node_color,
+            "cmap": cmap_nodes,
+            "vmin": vmin_nodes,
+            "vmax": vmax_nodes,
+            "ticks": node_ticks,
+            "label": node_colorbar_label,
+            "colorbar": show_colorbar,
+        }
+    }
+
+    _draw_network_with_curved_edges(
+        fig=fig,
+        ax=ax,
+        G=deepcopy(G),
+        pos=pos,
+        # dictionary of rings: {0:{'sizes':(N,)-array, 'color_array':(N,)-array
+        # or None, 'cmap':string,
+        node_rings=node_rings,
+        # 'vmin':float or None, 'vmax':float or None, 'label':string or None}}
+        node_labels=var_names,
+        node_label_size=node_label_size,
+        node_alpha=alpha,
+        standard_size=node_size,
+        node_aspect=node_aspect,
+        standard_cmap="OrRd",
+        standard_color_nodes="lightgrey",
+        standard_color_links="black",
+        log_sizes=False,
+        cmap_links=cmap_edges,
+        links_vmin=vmin_edges,
+        links_vmax=vmax_edges,
+        links_ticks=edge_ticks,
+        tick_label_size=tick_label_size,
+        # cmap_links_edges='YlOrRd', links_edges_vmin=-1., links_edges_vmax=1.,
+        # links_edges_ticks=.2, link_edge_colorbar_label='link_edge',
+        arrowstyle="simple",
+        arrowhead_size=arrowhead_size,
+        curved_radius=curved_radius,
+        label_fontsize=label_fontsize,
+        link_label_fontsize=link_label_fontsize,
+        link_colorbar_label=link_colorbar_label,
+        # network_lower_bound=network_lower_bound,
+        show_colorbar=show_colorbar,
+        # label_fraction=label_fraction,
+        special_nodes=special_nodes,
+        autodep_sig_lags=autodep_sig_lags,
+        show_autodependency_lags=show_autodependency_lags,
+        transform=transform,
+        special_links=special_links,
+    )
+
+    if save_name is not None:
+        pyplot.savefig(save_name, dpi=300)
+    else:
+        return fig, ax
+
+
+def _reverse_patt(patt):
+    """Inverts a link pattern"""
+
+    if patt == "":
+        return ""
+
+    left_mark, middle_mark, right_mark = patt[0], patt[1], patt[2]
+    if left_mark == "<":
+        new_right_mark = ">"
+    else:
+        new_right_mark = left_mark
+    if right_mark == ">":
+        new_left_mark = "<"
+    else:
+        new_left_mark = right_mark
+
+    return new_left_mark + middle_mark + new_right_mark
+
+    # if patt in ['---', 'o--', '--o', 'o-o', '']:
+    #     return patt[::-1]
+    # elif patt == '<->':
+    #     return '<->'
+    # elif patt == 'o->':
+    #     return '<-o'
+    # elif patt == '<-o':
+    #     return 'o->'
+    # elif patt == '-->':
+    #     return '<--'
+    # elif patt == '<--':
+    #     return '-->'
+
+
+def _check_matrices(graph, val_matrix, link_width, link_attribute):
+
+    if graph.dtype != "<U3":
+        # Transform to new graph data type U3
+        old_matrix = np.copy(graph)
+        graph = np.zeros(old_matrix.shape, dtype="<U3")
+        graph[:] = ""
+        for i, j, tau in zip(*np.where(old_matrix)):
+            if tau == 0:
+                if old_matrix[j, i, 0] == 0:
+                    graph[i, j, 0] = "-->"
+                    graph[j, i, 0] = "<--"
+                else:
+                    graph[i, j, 0] = "o-o"
+                    graph[j, i, 0] = "o-o"
+            else:
+                graph[i, j, tau] = "-->"
+    if graph.ndim == 4:
+        for i, j, taui, tauj in zip(*np.where(graph)):
+            if graph[i, j, taui, tauj] not in [
+                "---",
+                "o--",
+                "--o",
+                "o-o",
+                "o->",
+                "<-o",
+                "-->",
+                "<--",
+                "<->",
+                "x-o",
+                "o-x",
+                "x--",
+                "--x",
+                "x->",
+                "<-x",
+                "x-x",
+                "<-+",
+                "+->",
+                "<O>"   # contemporaneous cycle in union-graph
+            ]:
+                raise ValueError("Invalid graph entry.")
+            if graph[i, j, taui, tauj] != _reverse_patt(graph[j, i, tauj, taui]):
+                raise ValueError(
+                    "graph needs to have consistent entries: "
+                    "graph[i, j, taui, tauj] == _reverse_patt(graph[j, i, tauj, taui])")
+            if (
+                val_matrix is not None
+                and val_matrix[i, j, taui, tauj] != val_matrix[j, i, tauj, taui]
+            ):
+                raise ValueError(
+                    "val_matrix needs to have consistent entries: "
+                    "val_matrix[i, j, taui, tauj] == val_matrix[j, i, tauj, taui]")
+            if (
+                link_width is not None
+                and link_width[i, j, taui, tauj] != link_width[j, i, tauj, taui]
+            ):
+                raise ValueError(
+                    "link_width needs to have consistent entries: "
+                    "link_width[i, j, taui, tauj] == link_width[j, i, tauj, taui]")
+            if (
+                link_attribute is not None
+                and link_attribute[i, j, taui, tauj] != link_attribute[j, i, tauj, taui]
+            ):
+                raise ValueError(
+                    "link_attribute needs to have consistent entries: "
+                    "link_attribute[i, j, taui, tauj] == link_attribute[j, i, tauj, taui]")
+    else:
+        # print(graph[:,:,0])
+        # Assert that graph has valid and consistent lag-zero entries
+        for i, j, tau in zip(*np.where(graph)):
+            if tau == 0:
+                if graph[i, j, 0] != _reverse_patt(graph[j, i, 0]):
+                    raise ValueError(
+                        "graph needs to have consistent lag-zero links, but "
+                        " graph[%d,%d,0]=%s and graph[%d,%d,0]=%s)" %(i, j, graph[i, j, 0], j, i, graph[j, i, 0])
+                    )
+                if (
+                    val_matrix is not None
+                    and val_matrix[i, j, 0] != val_matrix[j, i, 0]
+                ):
+                    raise ValueError("val_matrix needs to be symmetric for lag-zero")
+                if (
+                    link_width is not None
+                    and link_width[i, j, 0] != link_width[j, i, 0]
+                ):
+                    raise ValueError("link_width needs to be symmetric for lag-zero")
+                if (
+                    link_attribute is not None
+                    and link_attribute[i, j, 0] != link_attribute[j, i, 0]
+                ):
+                    raise ValueError(
+                        "link_attribute needs to be symmetric for lag-zero"
+                    )
+
+            if graph[i, j, tau] not in [
+                "---",
+                "o--",
+                "--o",
+                "o-o",
+                "o->",
+                "<-o",
+                "-->",
+                "<--",
+                "<->",
+                "x-o",
+                "o-x",
+                "x--",
+                "--x",
+                "x->",
+                "<-x",
+                "x-x",
+                "<-+",
+                "+->",
+                "<O>"   # contemporaneous cycle in union-graph
+            ]:
+                raise ValueError("Invalid graph entry.")
+
+    if val_matrix is None:
+        # if graph.ndim == 4:
+        #     val_matrix = (graph != "").astype("int")
+        # else:
+            val_matrix = (graph != "").astype("int")
+
+    if link_width is not None and not np.all(link_width >= 0.0):
+        raise ValueError("link_width must be non-negative")
+
+    return graph, val_matrix, link_width, link_attribute
+
+
+def plot_time_series_graph(
+        graph,
+        val_matrix=None,
+        var_names=None,
+        fig_ax=None,
+        figsize=None,
+        link_colorbar_label="MCI",
+        save_name=None,
+        link_width=None,
+        link_attribute=None,
+        arrow_linewidth=4,
+        vmin_edges=-1,
+        vmax_edges=1.0,
+        edge_ticks=0.4,
+        cmap_edges="RdBu_r",
+        order=None,
+        node_size=0.1,
+        node_aspect=None,
+        arrowhead_size=20,
+        curved_radius=0.2,
+        label_fontsize=10,
+        tick_label_size=6,
+        alpha=1.0,
+        inner_edge_style="dashed",
+        link_matrix=None,
+        special_nodes=None,
+        node_classification=None,
+        # aux_graph=None,
+        standard_color_links='black',
+        standard_color_nodes='lightgrey',
+):
+    """Creates a time series graph.
+    This is still in beta. The time series graph's links are colored by
+    val_matrix.
+
+    Parameters
+    ----------
+    graph : string or bool array-like, optional (default: None)
+        Either string matrix providing graph or bool array providing only adjacencies
+        Either of shape (N, N, tau_max + 1) or as auxiliary graph of dims 
+        (N, N, tau_max+1, tau_max+1) describing auxADMG. 
+    val_matrix : array_like
+        Matrix of same shape as graph containing test statistic values.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    fig_ax : tuple of figure and axis object, optional (default: None)
+        Figure and axes instance. If None they are created.
+    figsize : tuple
+        Size of figure.
+    save_name : str, optional (default: None)
+        Name of figure file to save figure. If None, figure is shown in window.
+    link_colorbar_label : str, optional (default: 'MCI')
+        Test statistic label.
+    link_width : array-like, optional (default: None)
+        Array of val_matrix.shape specifying relative link width with maximum
+        given by arrow_linewidth. If None, all links have same width.
+    link_attribute : array-like, optional (default: None)
+        Array of graph.shape specifying specific in drawing the graph (for internal use).
+    order : list, optional (default: None)
+        order of variables from top to bottom.
+    arrow_linewidth : float, optional (default: 30)
+        Linewidth.
+    vmin_edges : float, optional (default: -1)
+        Link colorbar scale lower bound.
+    vmax_edges : float, optional (default: 1)
+        Link colorbar scale upper bound.
+    edge_ticks : float, optional (default: 0.4)
+        Link tick mark interval.
+    cmap_edges : str, optional (default: 'RdBu_r')
+        Colormap for links.
+    node_size : int, optional (default: 0.1)
+        Node size.
+    node_aspect : float, optional (default: None)
+        Ratio between the heigth and width of the varible nodes.
+    arrowhead_size : int, optional (default: 20)
+        Size of link arrow head. Passed on to FancyArrowPatch object.
+    curved_radius, float, optional (default: 0.2)
+        Curvature of links. Passed on to FancyArrowPatch object.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of colorbar labels.
+    alpha : float, optional (default: 1.)
+        Opacity.
+    node_label_size : int, optional (default: 10)
+        Fontsize of node labels.
+    link_label_fontsize : int, optional (default: 6)
+        Fontsize of link labels.
+    tick_label_size : int, optional (default: 6)
+        Fontsize of tick labels.
+    inner_edge_style : string, optional (default: 'dashed')
+        Style of inner_edge contemporaneous links.
+    special_nodes : dict
+        Dictionary of format {(i, -tau): 'blue', ...} to color special nodes.
+    node_classification : dict or None (default: None)
+        Dictionary of format {i: 'space_context', ...} to classify nodes into system, context, or dummy nodes.
+        Keys of the dictionary are from {0, ..., N-1} where N is the number of nodes.
+        Options for the values are "system", "time_context", "space_context", "time_dummy", or "space_dummy".
+        Space_contexts and dummy nodes need to be represented as a single node in the time series graph.
+        In case no value is supplied all nodes are treated as system nodes, i.e. are plotted in a time-resolved manner.
+    """
+
+    if link_matrix is not None:
+        raise ValueError("link_matrix is deprecated and replaced by graph array"
+                         " which is now returned by all methods.")
+
+    if fig_ax is None:
+        fig = pyplot.figure(figsize=figsize)
+        ax = fig.add_subplot(111, frame_on=False)
+    else:
+        fig, ax = fig_ax
+
+    if val_matrix is None:
+        no_coloring = True
+        cmap_edges = None
+    else:
+        no_coloring = False
+
+    (graph, val_matrix, link_width, link_attribute) = _check_matrices(
+        graph, val_matrix, link_width, link_attribute
+    )
+
+    if graph.ndim == 4:
+        N, N, dummy, _ = graph.shape
+        tau_max = dummy - 1
+        max_lag = tau_max + 1
+    else:
+        N, N, dummy = graph.shape
+        tau_max = dummy - 1
+        max_lag = tau_max + 1
+
+    if np.count_nonzero(graph == "") == graph.size:
+        if graph.ndim == 4:
+            graph[0, 1, 0, 0] = "---"
+        else:
+            graph[0, 1, 0] = "---"
+        no_links = True
+    else:
+        no_links = False
+
+    if var_names is None:
+        var_names = range(N)
+
+    if order is None:
+        order = range(N)
+
+    if set(order) != set(range(N)):
+        raise ValueError("order must be a permutation of range(N)")
+
+    def translate(row, lag):
+        return row * max_lag + lag
+
+    # Define graph links by absolute maximum (positive or negative like for
+    # partial correlation)
+    tsg = np.zeros((N * max_lag, N * max_lag))
+    tsg_val = np.zeros((N * max_lag, N * max_lag))
+    tsg_width = np.zeros((N * max_lag, N * max_lag))
+    tsg_style = np.zeros((N * max_lag, N * max_lag), dtype=graph.dtype)
+    if link_attribute is not None:
+        tsg_attr = np.zeros((N * max_lag, N * max_lag), dtype=link_attribute.dtype)
+
+    if graph.ndim == 4:
+        # 4-dimensional graphs represent the finite-time window projection of stationary 3-d graphs
+        # They are internally created in some classes
+        # Only draw link in one direction
+        for i, j, taui, tauj in np.column_stack(np.where(graph)):
+            tau = taui - tauj
+            # if tau <= 0 and j <= i:
+            if translate(i,   max_lag - 1 - taui) >= translate(j, max_lag-1-tauj):
+                continue
+            # print(max_lag, (i, -taui), (j, -tauj), aux_graph[i, j, taui, tauj])
+            # print(translate(i, max_lag - 1 - taui), translate(j, max_lag-1-tauj))
+            tsg[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = 1.0
+            tsg_val[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = val_matrix[i, j, taui, tauj]
+            tsg_style[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = graph[i, j, taui, tauj]
+            if link_width is not None:
+                tsg_width[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = link_width[i, j, taui, tauj] / link_width.max() * arrow_linewidth
+            if link_attribute is not None:
+                tsg_attr[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = link_attribute[i, j, taui, tauj] #'spurious'
+        # print(tsg_style)   
+            # print(tsg_style[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)] = graph[i, j, taui, tauj])
+            # print(max_lag, (i, -taui), (j, -tauj), graph[i, j, taui, tauj], tsg_style[translate(i,   max_lag - 1 - taui), translate(j, max_lag-1-tauj)])
+
+
+    else:
+      # Only draw link in one direction
+      # Remove lower triangle
+      link_matrix_tsg = np.copy(graph)
+      link_matrix_tsg[:, :, 0] = np.triu(graph[:, :, 0])
+
+      for i, j, tau in np.column_stack(np.where(link_matrix_tsg)):
+        for t in range(max_lag):
+            if (
+                0 <= translate(i, t - tau)
+                and translate(i, t - tau) % max_lag <= translate(j, t) % max_lag
+            ):
+
+                tsg[
+                    translate(i, t - tau), translate(j, t)
+                ] = 1.0  # val_matrix[i, j, tau]
+                tsg_val[translate(i, t - tau), translate(j, t)] = val_matrix[i, j, tau]
+                tsg_style[translate(i, t - tau), translate(j, t)] = graph[
+                    i, j, tau
+                ]
+                if link_width is not None:
+                    tsg_width[translate(i, t - tau), translate(j, t)] = (
+                        link_width[i, j, tau] / link_width.max() * arrow_linewidth
+                    )
+                if link_attribute is not None:
+                    tsg_attr[translate(i, t - tau), translate(j, t)] = link_attribute[
+                        i, j, tau
+                    ]
+
+
+    G = nx.DiGraph(tsg)
+
+    if special_nodes is not None:
+        special_nodes_tsg = {}
+        for node in special_nodes:
+            i, tau = node
+            if tau >= -tau_max:
+                special_nodes_tsg[translate(i, max_lag-1 + tau)] = special_nodes[node]
+
+        special_nodes = special_nodes_tsg
+
+    if node_classification is None:
+        node_classification = {i: "system" for i in range(N)}
+    node_classification_tsg = {}
+    for node in node_classification:
+        for tau in range(max_lag):
+            if tau == 0:
+                suffix = "_first"
+            elif tau == max_lag-1:
+                suffix = "_last"
+            else:
+                suffix = "_middle"
+            node_classification_tsg[translate(node, tau)] = node_classification[node] + suffix
+
+    # node_color = np.zeros(N)
+    # list of all strengths for color map
+    all_strengths = []
+    # Add attributes, contemporaneous and lagged links are handled separately
+    for (u, v, dic) in G.edges(data=True):
+        dic["no_links"] = no_links
+        if u != v:
+            # tau = np.abs((u - v) % max_lag)
+            # Determine neighbors in TSG
+            i = u // max_lag
+            taui = -(max_lag -1 - (u % max_lag))
+            j = v // max_lag
+            tauj = -(max_lag -1 - (v % max_lag))
+
+            if np.abs(i-j) <= 1 and np.abs(tauj-taui) <= 1:
+                inout = 'inner'
+                dic["inner_edge"] = True
+                dic["outer_edge"] = False
+            else:
+                inout = 'outer'
+                dic["inner_edge"] = False
+                dic["outer_edge"] = True
+
+            dic["%s_edge_type" % inout] = tsg_style[u, v]
+
+            dic["%s_edge_alpha" % inout] = alpha
+
+            if link_width is None:
+                # fraction of nonzero values
+                dic["%s_edge_width" % inout] = dic["%s_edge_width" % inout] = arrow_linewidth
+            else:
+                dic["%s_edge_width" % inout] = dic["%s_edge_width" % inout] = tsg_width[u, v]
+
+            if link_attribute is None:
+                dic["%s_edge_attribute" % inout] = None
+            else:
+                dic["%s_edge_attribute" % inout] = tsg_attr[u, v]
+
+            # value at argmax of average
+            if no_coloring:
+                dic["%s_edge_color" % inout] = None
+            else:
+                dic["%s_edge_color" % inout] = tsg_val[u, v]
+
+            all_strengths.append(dic["%s_edge_color" % inout])
+            dic["label"] = None
+        # print(u, v, dic)
+
+    # If no links are present, set value to zero
+    if len(all_strengths) == 0:
+        all_strengths = [0.0]
+
+    posarray = np.zeros((N * max_lag, 2))
+    for i in range(N * max_lag):
+        posarray[i] = np.array([(i % max_lag), (1.0 - i // max_lag)])
+
+    pos_tmp = {}
+    for i in range(N * max_lag):
+        # for n in range(N):
+        #     for tau in range(max_lag):
+        #         i = n*N + tau
+        pos_tmp[i] = np.array(
+            [
+                ((i % max_lag) - posarray.min(axis=0)[0])
+                / (posarray.max(axis=0)[0] - posarray.min(axis=0)[0]),
+                ((1.0 - i // max_lag) - posarray.min(axis=0)[1])
+                / (posarray.max(axis=0)[1] - posarray.min(axis=0)[1]),
+            ]
+        )
+        pos_tmp[i][np.isnan(pos_tmp[i])] = 0.0
+
+    pos = {}
+    for n in range(N):
+        for tau in range(max_lag):
+            pos[n * max_lag + tau] = pos_tmp[order[n] * max_lag + tau]
+
+    node_rings = {
+        0: {"sizes": None, "color_array": None, "label": "", "colorbar": False,}
+    }
+
+    node_labels = ["" for i in range(N * max_lag)]
+
+    if graph.ndim == 4 and val_matrix is None:
+        show_colorbar = False
+    else:
+        show_colorbar = True
+
+    _draw_network_with_curved_edges(
+        fig=fig,
+        ax=ax,
+        G=deepcopy(G),
+        pos=pos,
+        node_rings=node_rings,
+        node_labels=node_labels,
+        # node_label_size=node_label_size,
+        node_alpha=alpha,
+        standard_size=node_size,
+        node_aspect=node_aspect,
+        standard_cmap="OrRd",
+        standard_color_nodes=standard_color_nodes,
+        standard_color_links=standard_color_links,
+        log_sizes=False,
+        cmap_links=cmap_edges,
+        links_vmin=vmin_edges,
+        links_vmax=vmax_edges,
+        links_ticks=edge_ticks,
+        # link_label_fontsize=link_label_fontsize,
+        arrowstyle="simple",
+        arrowhead_size=arrowhead_size,
+        curved_radius=curved_radius,
+        label_fontsize=label_fontsize,
+        tick_label_size=tick_label_size,
+        label_fraction=0.5,
+        link_colorbar_label=link_colorbar_label,
+        inner_edge_curved=False,
+        # network_lower_bound=network_lower_bound,
+        # network_left_bound=label_space_left,
+        inner_edge_style=inner_edge_style,
+        special_nodes=special_nodes,
+        show_colorbar=show_colorbar,
+        node_classification=node_classification_tsg,
+        max_lag=max_lag,
+    )
+
+    for i in range(N):
+        trans = transforms.blended_transform_factory(ax.transAxes, ax.transData)
+        # trans = transforms.blended_transform_factory(fig.transFigure, ax.transData)
+        ax.text(
+            0.,
+            pos[order[i] * max_lag][1],
+            f"{var_names[order[i]]}",
+            fontsize=label_fontsize,
+            horizontalalignment="right",
+            verticalalignment="center",
+            transform=trans,
+        )
+
+    for tau in np.arange(max_lag - 1, -1, -1):
+        trans = transforms.blended_transform_factory(ax.transData, ax.transAxes)
+        # trans = transforms.blended_transform_factory(ax.transData, fig.transFigure)
+        if tau == max_lag - 1:
+            ax.text(
+                pos[tau][0],
+                1.0, # - label_space_top,
+                r"$t$",
+                fontsize=int(label_fontsize * 0.8),
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+        else:
+            ax.text(
+                pos[tau][0],
+                1.0, # - label_space_top,
+                r"$t-%s$" % str(max_lag - tau - 1),
+                fontsize=int(label_fontsize * 0.8),
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+
+    # pyplot.tight_layout()
+    if save_name is not None:
+        pyplot.savefig(save_name, dpi=300)
+    else:
+        return fig, ax
+
+
+def plot_mediation_time_series_graph(
+    path_node_array,
+    tsg_path_val_matrix,
+    var_names=None,
+    fig_ax=None,
+    figsize=None,
+    link_colorbar_label="link coeff. (edge color)",
+    node_colorbar_label="MCE (node color)",
+    save_name=None,
+    link_width=None,
+    arrow_linewidth=8,
+    vmin_edges=-1,
+    vmax_edges=1.0,
+    edge_ticks=0.4,
+    cmap_edges="RdBu_r",
+    order=None,
+    vmin_nodes=-1.0,
+    vmax_nodes=1.0,
+    node_ticks=0.4,
+    cmap_nodes="RdBu_r",
+    node_size=0.1,
+    node_aspect=None,
+    arrowhead_size=20,
+    curved_radius=0.2,
+    label_fontsize=12,
+    alpha=1.0,
+    node_label_size=12,
+    tick_label_size=6,
+    standard_color_links='black',
+    standard_color_nodes='lightgrey',
+):
+    """Creates a mediation time series graph plot.
+    This is still in beta. The time series graph's links are colored by
+    val_matrix.
+
+    Parameters
+    ----------
+    tsg_path_val_matrix : array_like
+        Matrix of shape (N*tau_max, N*tau_max) containing link weight values.
+    path_node_array: array_like
+        Array of shape (N,) containing node values.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    fig_ax : tuple of figure and axis object, optional (default: None)
+        Figure and axes instance. If None they are created.
+    figsize : tuple
+        Size of figure.
+    save_name : str, optional (default: None)
+        Name of figure file to save figure. If None, figure is shown in window.
+    link_colorbar_label : str, optional (default: 'link coeff. (edge color)')
+        Link colorbar label.
+    node_colorbar_label : str, optional (default: 'MCE (node color)')
+        Node colorbar label.
+    link_width : array-like, optional (default: None)
+        Array of val_matrix.shape specifying relative link width with maximum
+        given by arrow_linewidth. If None, all links have same width.
+    order : list, optional (default: None)
+        order of variables from top to bottom.
+    arrow_linewidth : float, optional (default: 30)
+        Linewidth.
+    vmin_edges : float, optional (default: -1)
+        Link colorbar scale lower bound.
+    vmax_edges : float, optional (default: 1)
+        Link colorbar scale upper bound.
+    edge_ticks : float, optional (default: 0.4)
+        Link tick mark interval.
+    cmap_edges : str, optional (default: 'RdBu_r')
+        Colormap for links.
+    vmin_nodes : float, optional (default: 0)
+        Node colorbar scale lower bound.
+    vmax_nodes : float, optional (default: 1)
+        Node colorbar scale upper bound.
+    node_ticks : float, optional (default: 0.4)
+        Node tick mark interval.
+    cmap_nodes : str, optional (default: 'OrRd')
+        Colormap for links.
+    node_size : int, optional (default: 0.1)
+        Node size.
+    node_aspect : float, optional (default: None)
+        Ratio between the heigth and width of the varible nodes.
+    arrowhead_size : int, optional (default: 20)
+        Size of link arrow head. Passed on to FancyArrowPatch object.
+    curved_radius, float, optional (default: 0.2)
+        Curvature of links. Passed on to FancyArrowPatch object.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of colorbar labels.
+    alpha : float, optional (default: 1.)
+        Opacity.
+    node_label_size : int, optional (default: 10)
+        Fontsize of node labels.
+    link_label_fontsize : int, optional (default: 6)
+        Fontsize of link labels.
+    """
+    N = len(path_node_array)
+    Nmaxlag = tsg_path_val_matrix.shape[0]
+    max_lag = Nmaxlag // N
+
+    if var_names is None:
+        var_names = range(N)
+
+    if fig_ax is None:
+        fig = pyplot.figure(figsize=figsize)
+        ax = fig.add_subplot(111, frame_on=False)
+    else:
+        fig, ax = fig_ax
+
+    if link_width is not None and not np.all(link_width >= 0.0):
+        raise ValueError("link_width must be non-negative")
+
+    if order is None:
+        order = range(N)
+
+    if set(order) != set(range(N)):
+        raise ValueError("order must be a permutation of range(N)")
+
+    def translate(row, lag):
+        return row * max_lag + lag
+
+    if np.count_nonzero(tsg_path_val_matrix) == np.count_nonzero(
+        np.diagonal(tsg_path_val_matrix)
+    ):
+        diagonal = True
+    else:
+        diagonal = False
+
+    if np.count_nonzero(tsg_path_val_matrix) == tsg_path_val_matrix.size or diagonal:
+        tsg_path_val_matrix[0, 1] = 1
+        no_links = True
+    else:
+        no_links = False
+
+    # Define graph links by absolute maximum (positive or negative like for
+    # partial correlation)
+    tsg = tsg_path_val_matrix
+    tsg_attr = np.zeros((N * max_lag, N * max_lag))
+
+    G = nx.DiGraph(tsg)
+
+    # node_color = np.zeros(N)
+    # list of all strengths for color map
+    all_strengths = []
+    # Add attributes, contemporaneous and lagged links are handled separately
+    for (u, v, dic) in G.edges(data=True):
+        dic["no_links"] = no_links
+        dic["outer_edge_attribute"] = None
+
+        if u != v:
+
+            if u % max_lag == v % max_lag:
+                dic["inner_edge"] = True
+                dic["outer_edge"] = False
+            else:
+                dic["inner_edge"] = False
+                dic["outer_edge"] = True
+
+            dic["inner_edge_alpha"] = alpha
+            dic["inner_edge_color"] = _get_absmax(
+                np.array([[[tsg[u, v], tsg[v, u]]]])
+            ).squeeze()
+            dic["inner_edge_width"] = arrow_linewidth
+            all_strengths.append(dic["inner_edge_color"])
+
+            dic["outer_edge_alpha"] = alpha
+
+            dic["outer_edge_width"] = arrow_linewidth
+
+            # value at argmax of average
+            dic["outer_edge_color"] = tsg[u, v]
+            all_strengths.append(dic["outer_edge_color"])
+            dic["label"] = None
+
+        # dic['outer_edge_edge'] = False
+        # dic['outer_edge_edgecolor'] = None
+        # dic['inner_edge_edge'] = False
+        # dic['inner_edge_edgecolor'] = None
+
+    # If no links are present, set value to zero
+    if len(all_strengths) == 0:
+        all_strengths = [0.0]
+
+    posarray = np.zeros((N * max_lag, 2))
+    for i in range(N * max_lag):
+        posarray[i] = np.array([(i % max_lag), (1.0 - i // max_lag)])
+
+    pos_tmp = {}
+    for i in range(N * max_lag):
+        # for n in range(N):
+        #     for tau in range(max_lag):
+        #         i = n*N + tau
+        pos_tmp[i] = np.array(
+            [
+                ((i % max_lag) - posarray.min(axis=0)[0])
+                / (posarray.max(axis=0)[0] - posarray.min(axis=0)[0]),
+                ((1.0 - i // max_lag) - posarray.min(axis=0)[1])
+                / (posarray.max(axis=0)[1] - posarray.min(axis=0)[1]),
+            ]
+        )
+        pos_tmp[i][np.isnan(pos_tmp[i])] = 0.0
+
+    pos = {}
+    for n in range(N):
+        for tau in range(max_lag):
+            pos[n * max_lag + tau] = pos_tmp[order[n] * max_lag + tau]
+
+    node_color = np.zeros(N * max_lag)
+    for inet, n in enumerate(range(0, N * max_lag, max_lag)):
+        node_color[n : n + max_lag] = path_node_array[inet]
+
+    # node_rings = {0: {'sizes': None, 'color_array': color_array,
+    #                   'label': '', 'colorbar': False,
+    #                   }
+    #               }
+
+    node_rings = {
+        0: {
+            "sizes": None,
+            "color_array": node_color,
+            "cmap": cmap_nodes,
+            "vmin": vmin_nodes,
+            "vmax": vmax_nodes,
+            "ticks": node_ticks,
+            "label": node_colorbar_label,
+            "colorbar": True,
+        }
+    }
+
+    # ] for v in range(max_lag)]
+    node_labels = ["" for i in range(N * max_lag)]
+
+    _draw_network_with_curved_edges(
+        fig=fig,
+        ax=ax,
+        G=deepcopy(G),
+        pos=pos,
+        # dictionary of rings: {0:{'sizes':(N,)-array, 'color_array':(N,)-array
+        # or None, 'cmap':string,
+        node_rings=node_rings,
+        # 'vmin':float or None, 'vmax':float or None, 'label':string or None}}
+        node_labels=node_labels,
+        node_label_size=node_label_size,
+        node_alpha=alpha,
+        standard_size=node_size,
+        node_aspect=node_aspect,
+        standard_cmap="OrRd",
+        standard_color_nodes=standard_color_nodes,
+        standard_color_links=standard_color_links,
+        log_sizes=False,
+        cmap_links=cmap_edges,
+        links_vmin=vmin_edges,
+        links_vmax=vmax_edges,
+        links_ticks=edge_ticks,
+        tick_label_size=tick_label_size,
+        # cmap_links_edges='YlOrRd', links_edges_vmin=-1., links_edges_vmax=1.,
+        # links_edges_ticks=.2, link_edge_colorbar_label='link_edge',
+        arrowhead_size=arrowhead_size,
+        curved_radius=curved_radius,
+        label_fontsize=label_fontsize,
+        label_fraction=0.5,
+        link_colorbar_label=link_colorbar_label,
+        inner_edge_curved=True,
+        # network_lower_bound=network_lower_bound
+        # inner_edge_style=inner_edge_style
+    )
+
+    for i in range(N):
+        trans = transforms.blended_transform_factory(ax.transAxes, ax.transData)
+        # trans = transforms.blended_transform_factory(fig.transFigure, ax.transData)
+        ax.text(
+            0.,
+            pos[order[i] * max_lag][1],
+            "%s" % str(var_names[order[i]]),
+            fontsize=label_fontsize,
+            horizontalalignment="right",
+            verticalalignment="center",
+            transform=trans,
+        )
+
+    for tau in np.arange(max_lag - 1, -1, -1):
+        trans = transforms.blended_transform_factory(ax.transData, ax.transAxes)
+        # trans = transforms.blended_transform_factory(ax.transData, fig.transFigure)
+        if tau == max_lag - 1:
+            ax.text(
+                pos[tau][0],
+                1.0, # - label_space_top,
+                r"$t$",
+                fontsize=label_fontsize,
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+        else:
+            ax.text(
+                pos[tau][0],
+                1.0, # - label_space_top,
+                r"$t-%s$" % str(max_lag - tau - 1),
+                fontsize=label_fontsize,
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+
+    # fig.subplots_adjust(left=0.1, right=.98, bottom=.25, top=.9)
+    # savestring = os.path.expanduser(save_name)
+    if save_name is not None:
+        pyplot.savefig(save_name)
+    else:
+        pyplot.show()
+
+
+def plot_mediation_graph(
+    path_val_matrix,
+    path_node_array=None,
+    var_names=None,
+    fig_ax=None,
+    figsize=None,
+    save_name=None,
+    link_colorbar_label="link coeff. (edge color)",
+    node_colorbar_label="MCE (node color)",
+    link_width=None,
+    node_pos=None,
+    arrow_linewidth=10.0,
+    vmin_edges=-1,
+    vmax_edges=1.0,
+    edge_ticks=0.4,
+    cmap_edges="RdBu_r",
+    vmin_nodes=-1.0,
+    vmax_nodes=1.0,
+    node_ticks=0.4,
+    cmap_nodes="RdBu_r",
+    node_size=0.3,
+    node_aspect=None,
+    arrowhead_size=20,
+    curved_radius=0.2,
+    label_fontsize=10,
+    tick_label_size=6,
+    lag_array=None,
+    alpha=1.0,
+    node_label_size=10,
+    link_label_fontsize=10,
+    # network_lower_bound=0.2,
+    standard_color_links='black',
+    standard_color_nodes='lightgrey',
+):
+    """Creates a network plot visualizing the pathways of a mediation analysis.
+    This is still in beta. The network is defined from non-zero entries in
+    ``path_val_matrix``.  Nodes denote variables, straight links contemporaneous
+    dependencies and curved arrows lagged dependencies. The node color denotes
+    the mediated causal effect (MCE) and the link color the value at the lag
+    with maximal link coefficient. The link label lists the lags with
+    significant dependency in order of absolute magnitude. The network can also
+    be plotted over a map drawn before on the same axis. Then the node positions
+    can be supplied in appropriate axis coordinates via node_pos.
+
+    Parameters
+    ----------
+    path_val_matrix : array_like
+        Matrix of shape (N, N, tau_max+1) containing link weight values.
+    path_node_array: array_like
+        Array of shape (N,) containing node values.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    fig_ax : tuple of figure and axis object, optional (default: None)
+        Figure and axes instance. If None they are created.
+    figsize : tuple
+        Size of figure.
+    save_name : str, optional (default: None)
+        Name of figure file to save figure. If None, figure is shown in window.
+    link_colorbar_label : str, optional (default: 'link coeff. (edge color)')
+        Link colorbar label.
+    node_colorbar_label : str, optional (default: 'MCE (node color)')
+        Node colorbar label.
+    link_width : array-like, optional (default: None)
+        Array of val_matrix.shape specifying relative link width with maximum
+        given by arrow_linewidth. If None, all links have same width.
+    node_pos : dictionary, optional (default: None)
+        Dictionary of node positions in axis coordinates of form
+        node_pos = {'x':array of shape (N,), 'y':array of shape(N)}. These
+        coordinates could have been transformed before for basemap plots. You can
+        also add a key 'transform':ccrs.PlateCarree() in order to plot graphs on 
+        a map using cartopy.
+    arrow_linewidth : float, optional (default: 30)
+        Linewidth.
+    vmin_edges : float, optional (default: -1)
+        Link colorbar scale lower bound.
+    vmax_edges : float, optional (default: 1)
+        Link colorbar scale upper bound.
+    edge_ticks : float, optional (default: 0.4)
+        Link tick mark interval.
+    cmap_edges : str, optional (default: 'RdBu_r')
+        Colormap for links.
+    vmin_nodes : float, optional (default: 0)
+        Node colorbar scale lower bound.
+    vmax_nodes : float, optional (default: 1)
+        Node colorbar scale upper bound.
+    node_ticks : float, optional (default: 0.4)
+        Node tick mark interval.
+    cmap_nodes : str, optional (default: 'OrRd')
+        Colormap for links.
+    node_size : int, optional (default: 0.3)
+        Node size.
+    node_aspect : float, optional (default: None)
+        Ratio between the heigth and width of the varible nodes.
+    arrowhead_size : int, optional (default: 20)
+        Size of link arrow head. Passed on to FancyArrowPatch object.
+    curved_radius, float, optional (default: 0.2)
+        Curvature of links. Passed on to FancyArrowPatch object.
+    label_fontsize : int, optional (default: 10)
+        Fontsize of colorbar labels.
+    alpha : float, optional (default: 1.)
+        Opacity.
+    node_label_size : int, optional (default: 10)
+        Fontsize of node labels.
+    link_label_fontsize : int, optional (default: 6)
+        Fontsize of link labels.
+    lag_array : array, optional (default: None)
+        Optional specification of lags overwriting np.arange(0, tau_max+1)
+    """
+    val_matrix = path_val_matrix
+
+    if fig_ax is None:
+        fig = pyplot.figure(figsize=figsize)
+        ax = fig.add_subplot(111, frame_on=False)
+    else:
+        fig, ax = fig_ax
+
+    if link_width is not None and not np.all(link_width >= 0.0):
+        raise ValueError("link_width must be non-negative")
+
+    N, N, dummy = val_matrix.shape
+    tau_max = dummy - 1
+
+    if np.count_nonzero(val_matrix) == np.count_nonzero(np.diagonal(val_matrix)):
+        diagonal = True
+    else:
+        diagonal = False
+
+    if np.count_nonzero(val_matrix) == val_matrix.size or diagonal:
+        val_matrix[0, 1, 0] = 1
+        no_links = True
+    else:
+        no_links = False
+
+    if var_names is None:
+        var_names = range(N)
+
+    # Define graph links by absolute maximum (positive or negative like for
+    # partial correlation)
+    # val_matrix[np.abs(val_matrix) < sig_thres] = 0.
+    graph = val_matrix != 0.0
+    net = _get_absmax(val_matrix)
+    G = nx.DiGraph(net)
+
+    node_color = np.zeros(N)
+    # list of all strengths for color map
+    all_strengths = []
+    # Add attributes, contemporaneous and lagged links are handled separately
+    for (u, v, dic) in G.edges(data=True):
+        dic["outer_edge_attribute"] = None
+        dic["no_links"] = no_links
+        # average lagfunc for link u --> v ANDOR u -- v
+        if tau_max > 0:
+            # argmax of absolute maximum
+            argmax = np.abs(val_matrix[u, v][1:]).argmax() + 1
+        else:
+            argmax = 0
+        if u != v:
+            # For contemp links masking or finite samples can lead to different
+            # values for u--v and v--u
+            # Here we use the  maximum for the width and weight (=color)
+            # of the link
+            # Draw link if u--v OR v--u at lag 0 is nonzero
+            # dic['inner_edge'] = ((np.abs(val_matrix[u, v][0]) >=
+            #                       sig_thres[u, v][0]) or
+            #                      (np.abs(val_matrix[v, u][0]) >=
+            #                       sig_thres[v, u][0]))
+            dic["inner_edge"] = graph[u, v, 0] or graph[v, u, 0]
+            dic["inner_edge_alpha"] = alpha
+            # value at argmax of average
+            if np.abs(val_matrix[u, v][0] - val_matrix[v, u][0]) > 0.0001:
+                print(
+                    "Contemporaneous I(%d; %d)=%.3f != I(%d; %d)=%.3f"
+                    % (u, v, val_matrix[u, v][0], v, u, val_matrix[v, u][0])
+                    + " due to conditions, finite sample effects or "
+                    "masking, here edge color = "
+                    "larger (absolute) value."
+                )
+            dic["inner_edge_color"] = _get_absmax(
+                np.array([[[val_matrix[u, v][0], val_matrix[v, u][0]]]])
+            ).squeeze()
+            if link_width is None:
+                dic["inner_edge_width"] = arrow_linewidth
+            else:
+                dic["inner_edge_width"] = (
+                    link_width[u, v, 0] / link_width.max() * arrow_linewidth
+                )
+
+            all_strengths.append(dic["inner_edge_color"])
+
+            if tau_max > 0:
+                # True if ensemble mean at lags > 0 is nonzero
+                # dic['outer_edge'] = np.any(
+                #     np.abs(val_matrix[u, v][1:]) >= sig_thres[u, v][1:])
+                dic["outer_edge"] = np.any(graph[u, v, 1:])
+            else:
+                dic["outer_edge"] = False
+            dic["outer_edge_alpha"] = alpha
+            if link_width is None:
+                # fraction of nonzero values
+                dic["outer_edge_width"] = arrow_linewidth
+            else:
+                dic["outer_edge_width"] = (
+                    link_width[u, v, argmax] / link_width.max() * arrow_linewidth
+                )
+
+            # value at argmax of average
+            dic["outer_edge_color"] = val_matrix[u, v][argmax]
+            all_strengths.append(dic["outer_edge_color"])
+
+            # Sorted list of significant lags (only if robust wrt
+            # d['min_ensemble_frac'])
+            if tau_max > 0:
+                lags = np.abs(val_matrix[u, v][1:]).argsort()[::-1] + 1
+                sig_lags = (np.where(graph[u, v, 1:])[0] + 1).tolist()
+            else:
+                lags, sig_lags = [], []
+            if lag_array is not None:
+                dic["label"] = ",".join([str(lag_array[l]) for l in lags if l in sig_lags])  #str([str(lag_array[l]) for l in lags if l in sig_lags])[1:-1].replace(" ", "")
+            else:
+                dic["label"] = ",".join([str(l) for l in lags if l in sig_lags]) # str([str(l) for l in lags if l in sig_lags])[1:-1].replace(" ", "")
+        else:
+            # Node color is max of average autodependency
+            node_color[u] = val_matrix[u, v][argmax]
+
+        # dic['outer_edge_edge'] = False
+        # dic['outer_edge_edgecolor'] = None
+        # dic['inner_edge_edge'] = False
+        # dic['inner_edge_edgecolor'] = None
+
+    node_color = path_node_array
+    # print node_color
+    # If no links are present, set value to zero
+    if len(all_strengths) == 0:
+        all_strengths = [0.0]
+
+    if node_pos is None:
+        pos = nx.circular_layout(deepcopy(G))
+    #            pos = nx.spring_layout(deepcopy(G))
+    else:
+        pos = {}
+        for i in range(N):
+            pos[i] = (node_pos["x"][i], node_pos["y"][i])
+
+    if node_pos is not None and 'transform' in node_pos:
+        transform = node_pos['transform']
+    else: transform = ax.transData
+
+    node_rings = {
+        0: {
+            "sizes": None,
+            "color_array": node_color,
+            "cmap": cmap_nodes,
+            "vmin": vmin_nodes,
+            "vmax": vmax_nodes,
+            "ticks": node_ticks,
+            "label": node_colorbar_label,
+            "colorbar": True,
+        }
+    }
+
+    _draw_network_with_curved_edges(
+        fig=fig,
+        ax=ax,
+        G=deepcopy(G),
+        pos=pos,
+        # dictionary of rings: {0:{'sizes':(N,)-array, 'color_array':(N,)-array
+        # or None, 'cmap':string,
+        node_rings=node_rings,
+        # 'vmin':float or None, 'vmax':float or None, 'label':string or None}}
+        node_labels=var_names,
+        node_label_size=node_label_size,
+        node_alpha=alpha,
+        standard_size=node_size,
+        node_aspect=node_aspect,
+        standard_cmap="OrRd",
+        standard_color_nodes=standard_color_nodes,
+        standard_color_links=standard_color_links,
+        log_sizes=False,
+        cmap_links=cmap_edges,
+        links_vmin=vmin_edges,
+        links_vmax=vmax_edges,
+        links_ticks=edge_ticks,
+        tick_label_size=tick_label_size,
+        # cmap_links_edges='YlOrRd', links_edges_vmin=-1., links_edges_vmax=1.,
+        # links_edges_ticks=.2, link_edge_colorbar_label='link_edge',
+        arrowhead_size=arrowhead_size,
+        curved_radius=curved_radius,
+        label_fontsize=label_fontsize,
+        link_label_fontsize=link_label_fontsize,
+        link_colorbar_label=link_colorbar_label,
+        # network_lower_bound=network_lower_bound,
+        # label_fraction=label_fraction,
+        # inner_edge_style=inner_edge_style
+        transform=transform
+    )
+
+    # fig.subplots_adjust(left=0.1, right=.9, bottom=.25, top=.95)
+    # savestring = os.path.expanduser(save_name)
+    if save_name is not None:
+        pyplot.savefig(save_name)
+    else:
+        pyplot.show()
+
+
+#
+#  Functions to plot time series graphs from links including ancestors
+#
+def plot_tsg(links, X, Y, Z=None, anc_x=None, anc_y=None, anc_xy=None):
+    """Plots TSG that is input in format (N*max_lag, N*max_lag).
+    Compared to the tigramite plotting function here links
+    X^i_{t-tau} --> X^j_t can be missing for different t'. Helpful to
+    visualize the conditioned TSG.
+    """
+
+    def varlag2node(var, lag):
+        """Translate from (var, lag) notation to node in TSG.
+        lag must be <= 0.
+        """
+        return var * max_lag + lag
+
+    def node2varlag(node):
+        """Translate from node in TSG to (var, -tau) notation.
+        Here tau is <= 0.
+        """
+        var = node // max_lag
+        tau = node % (max_lag) - (max_lag - 1)
+        return var, tau
+
+    def _get_minmax_lag(links):
+        """Helper function to retrieve tau_min and tau_max from links
+        """
+
+        N = len(links)
+
+        # Get maximum time lag
+        min_lag = np.inf
+        max_lag = 0
+        for j in range(N):
+            for link_props in links[j]:
+                var, lag = link_props[0]
+                coeff = link_props[1]
+                # func = link_props[2]
+                if coeff != 0.:
+                    min_lag = min(min_lag, abs(lag))
+                    max_lag = max(max_lag, abs(lag))
+        return min_lag, max_lag
+
+    def _links_to_tsg(link_coeffs, max_lag=None):
+        """Transform link_coeffs to time series graph.
+        TSG is of shape (N*max_lag, N*max_lag).
+        """
+        N = len(link_coeffs)
+
+        # Get maximum lag
+        min_lag_links, max_lag_links = _get_minmax_lag(link_coeffs)
+
+        # max_lag of TSG is max lag in links + 1 for the zero lag.
+        if max_lag is None:
+            max_lag = max_lag_links + 1
+
+        tsg = np.zeros((N * max_lag, N * max_lag))
+
+        for j in range(N):
+            for link_props in link_coeffs[j]:
+                i, lag = link_props[0]
+                tau = abs(lag)
+                coeff = link_props[1]
+                # func = link_props[2]
+                if coeff != 0.0:
+                    for t in range(max_lag):
+                        if (
+                            0 <= varlag2node(i, t - tau)
+                            and varlag2node(i, t - tau) % max_lag
+                            <= varlag2node(j, t) % max_lag
+                        ):
+                            tsg[varlag2node(i, t - tau), varlag2node(j, t)] = 1.0
+
+        return tsg
+
+    color_list = ["lightgrey", "grey", "black", "red", "blue", "orange"]
+    listcmap = ListedColormap(color_list)
+
+    N = len(links)
+
+    min_lag_links, max_lag_links = _get_minmax_lag(links)
+    max_lag = max_lag_links
+
+    for anc in X + Y:
+        max_lag = max(max_lag, abs(anc[1]))
+    for anc in Y:
+        max_lag = max(max_lag, abs(anc[1]))
+    if Z is not None:
+        for anc in Z:
+            max_lag = max(max_lag, abs(anc[1]))
+
+    if anc_x is not None:
+        for anc in anc_x:
+            max_lag = max(max_lag, abs(anc[1]))
+    if anc_y is not None:
+        for anc in anc_y:
+            max_lag = max(max_lag, abs(anc[1]))
+    if anc_xy is not None:
+        for anc in anc_xy:
+            max_lag = max(max_lag, abs(anc[1]))
+
+    max_lag = max_lag + 1
+
+    tsg = _links_to_tsg(links, max_lag=max_lag)
+
+    G = nx.DiGraph(tsg)
+
+    figsize = (3, 3)
+    link_colorbar_label = "MCI"
+    arrow_linewidth = 8.0
+    vmin_edges = -1
+    vmax_edges = 1.0
+    edge_ticks = 0.4
+    cmap_edges = "RdBu_r"
+    order = None
+    node_size = .1
+    arrowhead_size = 20
+    curved_radius = 0.2
+    label_fontsize = 10
+    alpha = 1.0
+    node_label_size = 10
+    # label_space_left = 0.1
+    # label_space_top = 0.0
+    # network_lower_bound = 0.2
+    inner_edge_style = "dashed"
+
+    node_color = np.ones(N * max_lag)  # , dtype = 'object')
+    node_color[:] = 0
+
+    if anc_x is not None:
+        for n in [varlag2node(itau[0], max_lag - 1 + itau[1]) for itau in anc_x]:
+            node_color[n] = 3
+    if anc_y is not None:
+        for n in [varlag2node(itau[0], max_lag - 1 + itau[1]) for itau in anc_y]:
+            node_color[n] = 4
+    if anc_xy is not None:
+        for n in [varlag2node(itau[0], max_lag - 1 + itau[1]) for itau in anc_xy]:
+            node_color[n] = 5
+
+    for x in X:
+        node_color[varlag2node(x[0], max_lag - 1 + x[1])] = 2
+    for y in Y:
+        node_color[varlag2node(y[0], max_lag - 1 + y[1])] = 2
+    if Z is not None:
+        for z in Z:
+            node_color[varlag2node(z[0], max_lag - 1 + z[1])] = 1
+
+    fig = pyplot.figure(figsize=figsize)
+    ax = fig.add_subplot(111, frame_on=False)
+    var_names = range(N)
+    order = range(N)
+
+    # list of all strengths for color map
+    all_strengths = []
+    # Add attributes, contemporaneous and lagged links are handled separately
+    for (u, v, dic) in G.edges(data=True):
+        if u != v:
+            if tsg[u, v] and tsg[v, u]:
+                dic["inner_edge"] = True
+                dic["outer_edge"] = False
+            else:
+                dic["inner_edge"] = False
+                dic["outer_edge"] = True
+
+            dic["inner_edge_alpha"] = alpha
+            dic["inner_edge_color"] = tsg[u, v]
+
+            dic["inner_edge_width"] = arrow_linewidth
+            dic["inner_edge_attribute"] = dic["outer_edge_attribute"] = None
+
+            all_strengths.append(dic["inner_edge_color"])
+            dic["outer_edge_alpha"] = alpha
+            dic["outer_edge_width"] = dic["inner_edge_width"] = arrow_linewidth
+
+            # value at argmax of average
+            dic["outer_edge_color"] = tsg[u, v]
+
+            all_strengths.append(dic["outer_edge_color"])
+            dic["label"] = None
+
+    # If no links are present, set value to zero
+    if len(all_strengths) == 0:
+        all_strengths = [0.0]
+
+    posarray = np.zeros((N * max_lag, 2))
+    for i in range(N * max_lag):
+        posarray[i] = np.array([(i % max_lag), (1.0 - i // max_lag)])
+
+    pos_tmp = {}
+    for i in range(N * max_lag):
+        pos_tmp[i] = np.array(
+            [
+                ((i % max_lag) - posarray.min(axis=0)[0])
+                / (posarray.max(axis=0)[0] - posarray.min(axis=0)[0]),
+                ((1.0 - i // max_lag) - posarray.min(axis=0)[1])
+                / (posarray.max(axis=0)[1] - posarray.min(axis=0)[1]),
+            ]
+        )
+        pos_tmp[i][np.isnan(pos_tmp[i])] = 0.0
+
+    pos = {}
+    for n in range(N):
+        for tau in range(max_lag):
+            pos[n * max_lag + tau] = pos_tmp[order[n] * max_lag + tau]
+
+    node_rings = {
+        0: {
+            "sizes": None,
+            "color_array": node_color,
+            "label": "",
+            "colorbar": False,
+            "cmap": listcmap,
+            "vmin": 0,
+            "vmax": len(color_list),
+        }
+    }
+
+    node_labels = ["" for i in range(N * max_lag)]
+
+    _draw_network_with_curved_edges(
+        fig=fig,
+        ax=ax,
+        G=deepcopy(G),
+        pos=pos,
+        node_rings=node_rings,
+        node_labels=node_labels,
+        node_label_size=node_label_size,
+        node_alpha=alpha,
+        standard_size=node_size,
+        node_aspect=None,
+        standard_cmap="OrRd",
+        standard_color_links='black',
+        standard_color_nodes='lightgrey',
+        log_sizes=False,
+        cmap_links=cmap_edges,
+        links_vmin=vmin_edges,
+        links_vmax=vmax_edges,
+        links_ticks=edge_ticks,
+        arrowstyle="simple",
+        arrowhead_size=arrowhead_size,
+        curved_radius=curved_radius,
+        label_fontsize=label_fontsize,
+        label_fraction=0.5,
+        link_colorbar_label=link_colorbar_label,
+        inner_edge_curved=True,
+        # network_lower_bound=network_lower_bound,
+        inner_edge_style=inner_edge_style,
+    )
+
+    for i in range(N):
+        trans = transforms.blended_transform_factory(ax.transAxes, ax.transData)
+        ax.text(
+            0.,
+            pos[order[i] * max_lag][1],
+            "%s" % str(var_names[order[i]]),
+            fontsize=label_fontsize,
+            horizontalalignment="right",
+            verticalalignment="center",
+            transform=trans,
+        )
+
+    for tau in np.arange(max_lag - 1, -1, -1):
+        trans = transforms.blended_transform_factory(ax.transData, ax.transAxes)
+        if tau == max_lag - 1:
+            ax.text(
+                pos[tau][0],
+                1.0, #- label_space_top,
+                r"$t$",
+                fontsize=int(label_fontsize * 0.7),
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+        else:
+            ax.text(
+                pos[tau][0],
+                1.0, # - label_space_top,
+                r"$t-%s$" % str(max_lag - tau - 1),
+                fontsize=int(label_fontsize * 0.7),
+                horizontalalignment="center",
+                verticalalignment="bottom",
+                transform=trans,
+            )
+
+    return fig, ax
+
+def write_csv(
+    graph,
+    save_name,
+    val_matrix=None,
+    var_names=None,
+    link_width=None,
+    link_attribute=None,
+    digits=5,
+):
+    """Writes all links in a graph to a csv file.
+    
+    Format is each link in a row as 'Variable i', 'Variable j', 'Time lag of i', 'Link type i --- j',
+    with optional further columns for entries in [val_matrix link_attribute, link_width].
+
+    Parameters
+    ----------
+    graph : string or bool array-like, optional (default: None)
+        Either string matrix providing graph or bool array providing only adjacencies
+        Must be of same shape as val_matrix. 
+    save_name : str
+        Name of figure file to save figure. If None, figure is shown in window.
+    val_matrix : array_like
+        Matrix of shape (N, N, tau_max+1) containing test statistic values.
+    var_names : list, optional (default: None)
+        List of variable names. If None, range(N) is used.
+    link_width : array-like, optional (default: None)
+        Array of val_matrix.shape specifying relative link width with maximum
+        given by arrow_linewidth. If None, all links have same width.
+    link_attribute : array-like, optional (default: None)
+        String array of val_matrix.shape specifying link attributes.
+    digits : int
+        Number of significant digits for writing link value and width.
+    """
+
+    graph = np.copy(graph.squeeze())
+
+    N = len(graph)
+
+    if val_matrix is None:
+        val_matrix_exists = false
+    else:
+        val_matrix_exists = True
+
+    if graph.ndim == 4:
+        raise ValueError("Time series graph of shape (N,N,tau_max+1,tau_max+1) cannot be represented by plot_graph,"
+                         " use plot_time_series_graph instead.")
+
+    if graph.ndim == 2:
+        # If a non-time series (N,N)-graph is given, insert a dummy dimension
+        graph = np.expand_dims(graph, axis = 2)
+
+    (graph, val_matrix, link_width, link_attribute) = _check_matrices(
+        graph, val_matrix, link_width, link_attribute)
+
+    if var_names is None:
+        var_names = range(N)
+
+
+    header = ['Variable i', 'Variable j', 'Time lag of i', 'Link type i --- j']
+    if val_matrix_exists:
+        header.append('Link value')
+    if link_attribute is not None:
+        header.append('Link attribute')
+    if link_width is not None:
+        header.append('Link width')
+
+
+    with open(save_name, 'w', encoding='UTF8', newline='') as f:
+        writer = csv.writer(f)
+
+        # write the header
+        writer.writerow(header)
+
+        # write the link data
+        for (i, j, tau) in zip(*np.where(graph!='')):
+            # Only consider contemporaneous links once
+            if tau > 0 or i <= j:
+                row = [str(var_names[i]), str(var_names[j]), f"{tau}", graph[i,j,tau]]
+                if val_matrix_exists:
+                    row.append(f"{val_matrix[i,j,tau]:.{digits}}")
+                if link_attribute is not None:
+                    row.append(link_attribute[i,j,tau])
+                if link_width is not None:
+                    row.append(f"{link_width[i,j,tau]:.{digits}}")
+
+                writer.writerow(row)
+
+
+if __name__ == "__main__":
+
+    import sys
+    matplotlib.rc('xtick', labelsize=6)
+    matplotlib.rc('ytick', labelsize=6)
+
+    # Consider some toy data
+    import tigramite
+    import tigramite.toymodels.structural_causal_processes as toys
+    import tigramite.data_processing as pp
+    from tigramite.causal_effects import CausalEffects
+
+
+    # T = 1000
+    def lin_f(x): return x
+    # auto_coeff = 0.3
+    # coeff = 1.
+    # links = {
+    #         0: [((0, -1), auto_coeff, lin_f)], 
+    #         1: [((1, -1), auto_coeff, lin_f), ((0, 0), coeff, lin_f)], 
+    #         2: [((2, -1), auto_coeff, lin_f), ((1, 0), coeff, lin_f)],
+    #         }
+    # data, nonstat = toys.structural_causal_process(links, T=T, 
+    #                             noises=None, seed=7)
+    # dataframe = pp.DataFrame(data, var_names=range(len(links)))
+
+    # links = {
+    #         0: [((0, -1), 1.5*auto_coeff, lin_f)], 
+    #         1: [((1, -1), 1.5*auto_coeff, lin_f), ((0, 0), 1.5*coeff, lin_f)], 
+    #         2: [((2, -1), 1.5*auto_coeff, lin_f), ((1, 0), 1.5*coeff, lin_f)],
+    #         }
+    # data2, nonstat = toys.structural_causal_process(links, T=T, 
+    #                             noises=None, seed=7)
+    # dataframe2 = pp.DataFrame(data2, var_names=range(len(links)))
+    # plot_densityplots(dataframe, name='test.pdf')
+
+    # N = len(links)
+
+
+    # parcorr = ParCorr(significance='analytic')
+    # pcmci = PCMCI(
+    #     dataframe=dataframe, 
+    #     cond_ind_test=parcorr,
+    #     verbosity=1)
+
+
+    correlations = np.random.rand(3, 3, 5) - 0.5 #pcmci.get_lagged_dependencies(tau_max=20, val_only=True)['val_matrix']
+    lag_func_matrix = plot_lagfuncs(val_matrix=correlations, setup_args={
+                        'label_space_left':0.05,
+                                    'minimum': 0.0,
+                                    'maximum':.05,
+                                    'x_base':5,
+                                    'y_base':.5})
+    plt.show()
+
+
+    # N = len(links)
+    # matrix = setup_density_matrix(N=N, var_names=dataframe.var_names)
+    # matrix.add_densityplot(dataframe=dataframe, 
+    #     # selected_dataset=0, 
+    #     **{
+    #     'label':'Weak',
+    #     'label_color':'blue',
+    #     "snskdeplot_args" : {'cmap':'Reds'},
+    #     }), #{'cmap':'Blues', 'alpha':0.3}})
+    # matrix.add_densityplot(dataframe=dataframe2, selected_dataset=0, 
+    #     **{'label':'Strong',
+    #     'label_color':'red',
+    #     "snskdeplot_args" : {'cmap':'Blues', 'alpha':0.3}})
+    # matrix.adjustfig(name='test.pdf')
+
+    # matrix = setup_scatter_matrix(N=dataframe.N, 
+    #     var_names=dataframe.var_names)
+    # matrix_lags = np.ones((3, 3)).astype('int')
+    # matrix.add_scatterplot(dataframe=dataframe, matrix_lags=matrix_lags,
+    #             label='ones', alpha=0.4)
+    # matrix_lags = 2*np.ones((3, 3)).astype('int')
+    # matrix.add_scatterplot(dataframe=dataframe, matrix_lags=matrix_lags, 
+    #     label='twos', color='red', alpha=0.4)
+
+    # matrix.savefig(name='scattertest.pdf')
+
+
+    # pyplot.show()
+    # sys.exit(0)
+
+
+    # val_matrix = np.zeros((4, 4, 3))
+
+    # # Complete test case
+    # graph = np.zeros((3,3,2), dtype='<U3')
+    # val_matrix = 0.*np.random.rand(*graph.shape)
+    # val_matrix[:,:,0] = 0.2
+    # graph[:] = ""
+    # # graph[0, 1, 0] = "<-+"
+    # # graph[1, 0, 0] = "+->"
+    # graph[0, 0, 1] = "-->"
+    # graph[1, 1, 1] = "-->"
+
+    # graph[0, 1, 1] = "+->"
+    # # graph[1, 0, 1] = "o-o"
+
+    # graph[1, 2, 0] = "<->"
+    # graph[2, 1, 0] = "<->"
+
+    # graph[0, 2, 0] = "x-x"
+    # # graph[2, 0, 0] = "x-x"
+    # nolinks = np.zeros(graph.shape)
+    # # nolinks[range(4), range(4), 1] = 1
+
+    # # graph = graph[:2, :2, :]
+
+    # # fig, axes = pyplot.subplots(nrows=1, ncols=1, figsize=(6, 5))
+
+
+    # # import cartopy.crs as ccrs
+    # graph = np.ones((5, 5, 2), dtype='<U3')
+    # graph[:] = ""
+    # graph[3, :, 1] = '+->' 
+
+    # fig = pyplot.figure(figsize=(8, 6))
+    # fig = pyplot.figure(figsize=(10, 5))
+    # ax = fig.add_subplot(1, 1, 1, projection=ccrs.Mollweide())
+    # make the map global rather than have it zoom in to
+    # the extents of any plotted data
+    # ax.set_global()
+    # ax.stock_img()
+    # ax.coastlines()
+    # # ymax = 1.
+    # node_pos = {'x':np.linspace(0, ymax, graph.shape[0]), 'y':np.linspace(0, ymax, graph.shape[0]),}
+    # node_pos = {'x':np.array([10,-20,80,-50,80]),
+    #             'y':np.array([-10,70,60,-40,50]), 
+    #         'transform':ccrs.PlateCarree(), # t.PlateCarree()
+    #         }
+
+    # plot_time_series_graph(graph=graph,
+    #     # fig_ax = (fig, ax),
+    #     # val_matrix=val_matrix,
+    #     # figsize=(5, 5),
+    #     # var_names = ['Var %s' %i for i in range(len(graph))],
+    #     # arrow_linewidth=6,
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     # # network_lower_bound=network_lower_bound,
+    #     save_name="tsg_test.pdf"
+    #     )
+    # pyplot.tight_layout()
+
+    # network_lower_bound = 0.
+    # show_colorbar=True
+    # plot_graph(graph=graph,
+    #     fig_ax = (fig, ax),
+    #     node_pos = node_pos,
+    #     node_size = 20,
+    #     # val_matrix=val_matrix,
+    #     # figsize=(5, 5),
+    #     # var_names = ['Var %s' %i for i in range(len(graph))],
+    #     # arrow_linewidth=6,
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     # # network_lower_bound=network_lower_bound,
+    #     save_name="tsg_test.pdf"
+    #     )
+    # pyplot.tight_layout()
+    # axes[0,0].scatter(np.random.rand(100), np.random.rand(100))
+
+    # plot_graph(graph=graph,
+    #     fig_ax = (fig, axes[0,0]),
+    #     val_matrix=val_matrix,
+    #     # figsize=(5, 5),
+    #     var_names = ['Variable %s' %i for i in range(len(graph))],
+    #     arrow_linewidth=6,
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     # save_name="tsg_test.pdf"
+    #     )
+    # plot_graph(graph=graph,
+    #     fig_ax = (fig, axes[0,1]),
+    #     val_matrix=val_matrix,
+    #     var_names = ['Var %s' %i for i in range(len(graph))],
+    #     arrow_linewidth=6,
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     )
+    # plot_graph(graph=graph,
+    #     fig_ax = (fig, axes[1,0]),
+    #     val_matrix=val_matrix,
+    #     var_names = ['Var %s' %i for i in range(len(graph))],
+    #     arrow_linewidth=6,
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     )
+    # plot_graph(graph=graph,
+    #     fig_ax = (fig, axes[1,1]),
+    #     val_matrix=val_matrix,
+    #     var_names = ['Var %s' %i for i in range(len(graph))],
+    #     arrow_linewidth=6,
+    #     n
+    #     # label_space_left = label_space_left,
+    #     # label_space_top = label_space_top,
+    #     )
+    # # pyplot.subplots_adjust(wspace=0.3, hspace=0.2)
+    # pyplot.tight_layout()
+    # pyplot.savefig("test.pdf")
+
+    # def lin_f(x): return x
+
+    # links_coeffs = {0: [((0, -1), 0.3, lin_f)], #, ((1, -1), 0.5, lin_f)],
+    #             1: [((1, -1), 0.3, lin_f), ((0, 0), 0.7, lin_f), ((2, -1), 0.5, lin_f)],
+    #             2: [],
+    #             3: [((3, -1), 0., lin_f), ((2, 0), 0.6, lin_f),]
+    #             }
+    # graph = CausalEffects.get_graph_from_dict(links_coeffs, tau_max=None)
+
+    # val_matrix = np.random.randn(*graph.shape)
+    # val_matrix[:,:,0] = 0.
+    # write_csv(graph=graph,
+    #     val_matrix=val_matrix,
+    #     var_names=[r'$X^{%d}$' %i for i in range(graph.shape[0])],
+    #     link_width=np.ones(graph.shape),
+    #     link_attribute = np.ones(graph.shape, dtype='<U10'),
+    #     save_name='test.csv')
+
+    # # print(graph)
+    # X = [(0,-1)]
+    # Y = [(1,0)]
+    # causal_effects = CausalEffects(graph, graph_type='stationary_dag', X=X, Y=Y, S=None, 
+    #                                hidden_variables=[(2, 0), (2, -1), (2, -2)], 
+    #                                verbosity=0)
+
+    # pyplot.show()