arviz 0.23.1__py3-none-any.whl → 1.0.0rc0__py3-none-any.whl

arviz/plots/parallelplot.py

@@ -1,204 +0,0 @@
-"""Parallel coordinates plot showing posterior points with and without divergences marked."""
-
-import numpy as np
-from scipy.stats import rankdata
-
-from ..data import convert_to_dataset
-from ..labels import BaseLabeller
-from ..sel_utils import xarray_to_ndarray
-from ..rcparams import rcParams
-from ..stats.stats_utils import stats_variance_2d as svar
-from ..utils import _numba_var, _var_names, get_coords
-from .plot_utils import get_plotting_function
-
-
-def plot_parallel(
-    data,
-    var_names=None,
-    filter_vars=None,
-    coords=None,
-    figsize=None,
-    textsize=None,
-    legend=True,
-    colornd="k",
-    colord="C1",
-    shadend=0.025,
-    labeller=None,
-    ax=None,
-    norm_method=None,
-    backend=None,
-    backend_config=None,
-    backend_kwargs=None,
-    show=None,
-):
-    """
-    Plot parallel coordinates plot showing posterior points with and without divergences.
-
-    Described by https://arxiv.org/abs/1709.01449
-
-    Parameters
-    ----------
-    data: obj
-        Any object that can be converted to an :class:`arviz.InferenceData` object
-        refer to documentation of :func:`arviz.convert_to_dataset` for details
-    var_names: list of variable names
-        Variables to be plotted, if `None` all variables are plotted. Can be used to change the
-        order of the plotted variables. Prefix the variables by ``~`` when you want to exclude
-        them from the plot.
-    filter_vars: {None, "like", "regex"}, optional, default=None
-        If `None` (default), interpret var_names as the real variables names. If "like",
-        interpret var_names as substrings of the real variables names. If "regex",
-        interpret var_names as regular expressions on the real variables names. A la
-        ``pandas.filter``.
-    coords: mapping, optional
-        Coordinates of ``var_names`` to be plotted.
-        Passed to :meth:`xarray.Dataset.sel`.
-    figsize: tuple
-        Figure size. If None it will be defined automatically.
-    textsize: float
-        Text size scaling factor for labels, titles and lines. If None it will be autoscaled based
-        on ``figsize``.
-    legend: bool
-        Flag for plotting legend (defaults to True)
-    colornd: valid matplotlib color
-        color for non-divergent points. Defaults to 'k'
-    colord: valid matplotlib color
-        color for divergent points. Defaults to 'C1'
-    shadend: float
-        Alpha blending value for non-divergent points, between 0 (invisible) and 1 (opaque).
-        Defaults to .025
-    labeller : labeller instance, optional
-        Class providing the method ``make_label_vert`` to generate the labels in the plot.
-        Read the :ref:`label_guide` for more details and usage examples.
-    ax: axes, optional
-        Matplotlib axes or bokeh figures.
-    norm_method: str
-        Method for normalizing the data. Methods include normal, minmax and rank.
-        Defaults to none.
-    backend: str, optional
-        Select plotting backend {"matplotlib","bokeh"}. Default "matplotlib".
-    backend_config: dict, optional
-        Currently specifies the bounds to use for bokeh axes.
-        Defaults to value set in ``rcParams``.
-    backend_kwargs: bool, optional
-        These are kwargs specific to the backend being used, passed to
-        :func:`matplotlib.pyplot.subplots` or
-        :func:`bokeh.plotting.figure`.
-    show: bool, optional
-        Call backend show function.
-
-    Returns
-    -------
-    axes: matplotlib axes or bokeh figures
-
-    See Also
-    --------
-    plot_pair : Plot a scatter, kde and/or hexbin matrix with (optional) marginals on the diagonal.
-    plot_trace : Plot distribution (histogram or kernel density estimates) and sampled values
-                 or rank plot
-
-    Examples
-    --------
-    Plot default parallel plot
-
-    .. plot::
-        :context: close-figs
-
-        >>> import arviz as az
-        >>> data = az.load_arviz_data('centered_eight')
-        >>> az.plot_parallel(data, var_names=["mu", "tau"])
-
-
-    Plot parallel plot with normalization
-
-    .. plot::
-        :context: close-figs
-
-        >>> az.plot_parallel(data, var_names=["theta", "tau", "mu"], norm_method="normal")
-
-    Plot parallel plot with minmax
-
-    .. plot::
-        :context: close-figs
-
-        >>> ax = az.plot_parallel(data, var_names=["theta", "tau", "mu"], norm_method="minmax")
-        >>> ax.set_xticklabels(ax.get_xticklabels(), rotation=45)
-
-    Plot parallel plot with rank
-
-    .. plot::
-        :context: close-figs
-
-        >>> ax = az.plot_parallel(data, var_names=["theta", "tau", "mu"], norm_method="rank")
-        >>> ax.set_xticklabels(ax.get_xticklabels(), rotation=45)
-    """
-    if coords is None:
-        coords = {}
-
-    if labeller is None:
-        labeller = BaseLabeller()
-
-    # Get diverging draws and combine chains
-    divergent_data = convert_to_dataset(data, group="sample_stats")
-    _, diverging_mask = xarray_to_ndarray(
-        divergent_data,
-        var_names=("diverging",),
-        combined=True,
-    )
-    diverging_mask = np.squeeze(diverging_mask)
-
-    # Get posterior draws and combine chains
-    posterior_data = convert_to_dataset(data, group="posterior")
-    var_names = _var_names(var_names, posterior_data, filter_vars)
-    var_names, _posterior = xarray_to_ndarray(
-        get_coords(posterior_data, coords),
-        var_names=var_names,
-        combined=True,
-        label_fun=labeller.make_label_vert,
-    )
-    if len(var_names) < 2:
-        raise ValueError("Number of variables to be plotted must be 2 or greater.")
-    if norm_method is not None:
-        if norm_method == "normal":
-            mean = np.mean(_posterior, axis=1)
-            if _posterior.ndim <= 2:
-                standard_deviation = np.sqrt(_numba_var(svar, np.var, _posterior, axis=1))
-            else:
-                standard_deviation = np.std(_posterior, axis=1)
-            for i in range(0, np.shape(mean)[0]):
-                _posterior[i, :] = (_posterior[i, :] - mean[i]) / standard_deviation[i]
-        elif norm_method == "minmax":
-            min_elem = np.min(_posterior, axis=1)
-            max_elem = np.max(_posterior, axis=1)
-            for i in range(0, np.shape(min_elem)[0]):
-                _posterior[i, :] = ((_posterior[i, :]) - min_elem[i]) / (max_elem[i] - min_elem[i])
-        elif norm_method == "rank":
-            _posterior = rankdata(_posterior, axis=1, method="average")
-        else:
-            raise ValueError(f"{norm_method} is not supported. Use normal, minmax or rank.")
-
-    parallel_kwargs = dict(
-        ax=ax,
-        colornd=colornd,
-        colord=colord,
-        shadend=shadend,
-        diverging_mask=diverging_mask,
-        posterior=_posterior,
-        textsize=textsize,
-        var_names=var_names,
-        legend=legend,
-        figsize=figsize,
-        backend_kwargs=backend_kwargs,
-        backend_config=backend_config,
-        show=show,
-    )
-
-    if backend is None:
-        backend = rcParams["plot.backend"]
-    backend = backend.lower()
-
-    # TODO: Add backend kwargs
-    plot = get_plotting_function("plot_parallel", "parallelplot", backend)
-    ax = plot(**parallel_kwargs)
-
-    return ax