Source code for arviz.plots.kdeplot

# pylint: disable=unexpected-keyword-arg
"""One-dimensional kernel density estimate plots."""
import warnings

import xarray as xr

from import InferenceData
from ..rcparams import rcParams
from ..stats.density_utils import _fast_kde_2d, kde, _find_hdi_contours
from .plot_utils import get_plotting_function

[docs]def plot_kde( values, values2=None, cumulative=False, rug=False, label=None, bw="default", adaptive=False, quantiles=None, rotated=False, contour=True, hdi_probs=None, fill_last=False, figsize=None, textsize=None, plot_kwargs=None, fill_kwargs=None, rug_kwargs=None, contour_kwargs=None, contourf_kwargs=None, pcolormesh_kwargs=None, is_circular=False, ax=None, legend=True, backend=None, backend_kwargs=None, show=None, return_glyph=False, **kwargs ): """1D or 2D KDE plot taking into account boundary conditions. Parameters ---------- values : array-like Values to plot values2 : array-like, optional Values to plot. If present, a 2D KDE will be estimated cumulative : bool If true plot the estimated cumulative distribution function. Defaults to False. Ignored for 2D KDE rug : bool If True adds a rugplot. Defaults to False. Ignored for 2D KDE label : string Text to include as part of the legend bw: float or str, optional If numeric, indicates the bandwidth and must be positive. If str, indicates the method to estimate the bandwidth and must be one of "scott", "silverman", "isj" or "experimental" when ``is_circular`` is False and "taylor" (for now) when ``is_circular`` is True. Defaults to "default" which means "experimental" when variable is not circular and "taylor" when it is. adaptive: bool, optional. If True, an adaptative bandwidth is used. Only valid for 1D KDE. Defaults to False. quantiles : list Quantiles in ascending order used to segment the KDE. Use [.25, .5, .75] for quartiles. Defaults to None. rotated : bool Whether to rotate the 1D KDE plot 90 degrees. contour : bool If True plot the 2D KDE using contours, otherwise plot a smooth 2D KDE. Defaults to True. hdi_probs : list Plots highest density credibility regions for the provided probabilities for a 2D KDE. Defaults to matplotlib chosen levels with no fixed probability associated. fill_last : bool If True fill the last contour of the 2D KDE plot. Defaults to False. 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``. Not implemented for bokeh backend. plot_kwargs : dict Keywords passed to the pdf line of a 1D KDE. See :meth:`mpl:matplotlib.axes.Axes.plot` or :meth:`bokeh:bokeh.plotting.Figure.line` for a description of accepted values. fill_kwargs : dict Keywords passed to the fill under the line (use ``fill_kwargs={'alpha': 0}`` to disable fill). Ignored for 2D KDE. Passed to :meth:`bokeh.plotting.Figure.patch`. rug_kwargs : dict Keywords passed to the rug plot. Ignored if ``rug=False`` or for 2D KDE Use ``space`` keyword (float) to control the position of the rugplot. The larger this number the lower the rugplot. Passed to :class:`bokeh:bokeh.models.glyphs.Scatter`. contour_kwargs : dict Keywords passed to :meth:`mpl:matplotlib.axes.Axes.contour` to draw contour lines or :meth:`bokeh.plotting.Figure.patch`. Ignored for 1D KDE. contourf_kwargs : dict Keywords passed to :meth:`mpl:matplotlib.axes.Axes.contourf` to draw filled contours. Ignored for 1D KDE. pcolormesh_kwargs : dict Keywords passed to :meth:`mpl:matplotlib.axes.Axes.pcolormesh` or :meth:`bokeh.plotting.Figure.image`. Ignored for 1D KDE. is_circular : {False, True, "radians", "degrees"}. Default False. Select input type {"radians", "degrees"} for circular histogram or KDE plot. If True, default input type is "radians". When this argument is present, it interprets ``values`` is a circular variable measured in radians and a circular KDE is used. Inputs in "degrees" will undergo an internal conversion to radians. ax: axes, optional Matplotlib axes or bokeh figures. legend : bool Add legend to the figure. By default True. backend: str, optional Select plotting backend {"matplotlib","bokeh"}. Default "matplotlib". backend_kwargs: bool, optional These are kwargs specific to the backend being used, passed to :func:`matplotlib.pyplot.subplots` or :func:`bokeh.plotting.figure`. For additional documentation check the plotting method of the backend. show : bool, optional Call backend show function. return_glyph : bool, optional Internal argument to return glyphs for bokeh Returns ------- axes : matplotlib.Axes or bokeh.plotting.Figure Object containing the kde plot glyphs : list, optional Bokeh glyphs present in plot. Only provided if ``return_glyph`` is True. See Also -------- kde : One dimensional density estimation. plot_dist : Plot distribution as histogram or kernel density estimates. Examples -------- Plot default KDE .. plot:: :context: close-figs >>> import arviz as az >>> non_centered = az.load_arviz_data('non_centered_eight') >>> mu_posterior = np.concatenate(non_centered.posterior["mu"].values) >>> tau_posterior = np.concatenate(non_centered.posterior["tau"].values) >>> az.plot_kde(mu_posterior) Plot KDE with rugplot .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, rug=True) Plot KDE with adaptive bandwidth .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, adaptive=True) Plot KDE with a different bandwidth estimator .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, bw="scott") Plot KDE with a bandwidth specified manually .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, bw=0.4) Plot KDE for a circular variable .. plot:: :context: close-figs >>> rvs = np.random.vonmises(mu=np.pi, kappa=2, size=500) >>> az.plot_kde(rvs, is_circular=True) Plot a cumulative distribution .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, cumulative=True) Rotate plot 90 degrees .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, rotated=True) Plot 2d contour KDE .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, values2=tau_posterior) Plot 2d contour KDE, without filling and contour lines using viridis cmap .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, values2=tau_posterior, ... contour_kwargs={"colors":None, "cmap"}, ... contourf_kwargs={"alpha":0}); Plot 2d contour KDE, set the number of levels to 3. .. plot:: :context: close-figs >>> az.plot_kde( ... mu_posterior, values2=tau_posterior, ... contour_kwargs={"levels":3}, contourf_kwargs={"levels":3} ... ); Plot 2d contour KDE with 30%, 60% and 90% HDI contours. .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, values2=tau_posterior, hdi_probs=[0.3, 0.6, 0.9]) Plot 2d smooth KDE .. plot:: :context: close-figs >>> az.plot_kde(mu_posterior, values2=tau_posterior, contour=False) """ if isinstance(values, xr.Dataset): raise ValueError( "Xarray dataset object detected.Use plot_posterior, plot_density" "or plot_pair instead of plot_kde" ) if isinstance(values, InferenceData): raise ValueError( " Inference Data object detected. Use plot_posterior " "or plot_pair instead of plot_kde" ) if values2 is None: if bw == "default": if is_circular: bw = "taylor" else: bw = "experimental" grid, density = kde(values, is_circular, bw=bw, adaptive=adaptive, cumulative=cumulative) lower, upper = grid[0], grid[-1] if cumulative: density_q = density else: density_q = density.cumsum() / density.sum() # This is just a hack placeholder for now xmin, xmax, ymin, ymax, gridsize = [None] * 5 else: gridsize = (128, 128) if contour else (256, 256) density, xmin, xmax, ymin, ymax = _fast_kde_2d(values, values2, gridsize=gridsize) if hdi_probs is not None: # Check hdi probs are within bounds (0, 1) if min(hdi_probs) <= 0 or max(hdi_probs) >= 1: raise ValueError("Highest density interval probabilities must be between 0 and 1") # Calculate contour levels and sort for matplotlib contour_levels = _find_hdi_contours(density, hdi_probs) contour_levels.sort() contour_level_list = [0] + list(contour_levels) + [density.max()] # Add keyword arguments to contour, contourf if contour_kwargs is None: contour_kwargs = {"levels": contour_level_list} else: if "levels" in contour_kwargs: warnings.warn( "Both 'levels' in contour_kwargs and 'hdi_probs' have been specified." "Using 'hdi_probs' in favor of 'levels'.", UserWarning, ) contour_kwargs["levels"] = contour_level_list if contourf_kwargs is None: contourf_kwargs = {"levels": contour_level_list} else: if "levels" in contourf_kwargs: warnings.warn( "Both 'levels' in contourf_kwargs and 'hdi_probs' have been specified." "Using 'hdi_probs' in favor of 'levels'.", UserWarning, ) contourf_kwargs["levels"] = contour_level_list lower, upper, density_q = [None] * 3 kde_plot_args = dict( # Internal API density=density, lower=lower, upper=upper, density_q=density_q, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax, gridsize=gridsize, # User Facing API that can be simplified values=values, values2=values2, rug=rug, label=label, quantiles=quantiles, rotated=rotated, contour=contour, fill_last=fill_last, figsize=figsize, textsize=textsize, plot_kwargs=plot_kwargs, fill_kwargs=fill_kwargs, rug_kwargs=rug_kwargs, contour_kwargs=contour_kwargs, contourf_kwargs=contourf_kwargs, pcolormesh_kwargs=pcolormesh_kwargs, is_circular=is_circular, ax=ax, legend=legend, backend_kwargs=backend_kwargs, show=show, return_glyph=return_glyph, **kwargs, ) if backend is None: backend = rcParams["plot.backend"] backend = backend.lower() # TODO: Add backend kwargs plot = get_plotting_function("plot_kde", "kdeplot", backend) ax = plot(**kde_plot_args) return ax