Add rootogram

References.md

@@ -48,5 +48,12 @@ See https://github.com/arviz-devs/arviz-stats/issues/56
 
     References
     ----------
-    .. [1] Betancourt. Diagnosing Suboptimal Cotangent Disintegrations in
-        Hamiltonian Monte Carlo. (2016) https://arxiv.org/abs/1604.00695
+    .. [1] Betancourt. *Diagnosing Suboptimal Cotangent Disintegrations in
+        Hamiltonian Monte Carlo*. (2016) https://arxiv.org/abs/1604.00695
+
+## Rootograms
+
+    References
+    ----------
+    .. [1] Kleiber C, Zeileis A. *Visualizing Count Data Regressions Using Rootograms*. 
+        The American Statistician, 70(3). (2016) https://doi.org/10.1080/00031305.2016.1173590

docs/source/api/plots.rst

@@ -23,8 +23,9 @@ A complementary introduction and guide to ``plot_...`` functions is available at
    plot_ess
    plot_ess_evolution
    plot_forest
-   plot_ppc_pava
    plot_ppc_dist
+   plot_ppc_pava
+   plot_ppc_rootogram
    plot_psense_dist
    plot_psense_quantities
    plot_ridge

docs/source/gallery/model_criticism/plot_ppc_rootogram.py

@@ -0,0 +1,23 @@
+"""
+# Rootogram plot
+
+Rootogram for the posterior predictive and observed data.
+
+---
+
+:::{seealso}
+API Documentation: {func}`~arviz_plots.plot_ppc_rootogram`
+:::
+"""
+from arviz_base import load_arviz_data
+
+import arviz_plots as azp
+
+azp.style.use("arviz-variat")
+
+dt = load_arviz_data("rugby")
+pc = azp.plot_ppc_rootogram(
+    dt,
+    backend="none",
+)
+pc.show()

src/arviz_plots/backend/bokeh/__init__.py

@@ -390,6 +390,26 @@ def hline(y, target, *, color=unset, alpha=unset, width=unset, linestyle=unset,
     return span_element
 
 
+def ciliney(
+    x,
+    y_bottom,
+    y_top,
+    target,
+    *,
+    color=unset,
+    alpha=unset,
+    width=unset,
+    linestyle=unset,
+    **artist_kws,
+):
+    """Interface to bokeh for a line from y_bottom to y_top at given value of x."""
+    kwargs = {"color": color, "alpha": alpha, "line_width": width, "line_dash": linestyle}
+    x = np.atleast_1d(x)
+    y_bottom = np.atleast_1d(y_bottom)
+    y_top = np.atleast_1d(y_top)
+    return target.segment(x0=x, x1=x, y0=y_bottom, y1=y_top, **_filter_kwargs(kwargs, artist_kws))
+
+
 # general plot appeareance
 def title(string, target, *, size=unset, color=unset, **artist_kws):
     """Interface to bokeh for adding a title to a plot."""
@@ -473,3 +493,8 @@ def remove_axis(target, axis="y"):
         target.axis.visible = False
     else:
         raise ValueError(f"axis must be one of 'x', 'y' or 'both', got '{axis}'")
+
+
+def set_y_scale(target, scale):
+    """Interface to matplotlib for setting the y scale of a plot."""
+    target.set_yscale(scale)

src/arviz_plots/backend/matplotlib/__init__.py

@@ -1,3 +1,4 @@
+# pylint: disable=no-self-use
 """Matplotlib interface layer.
 
 Notes
@@ -9,7 +10,10 @@
 import warnings
 from typing import Any, Dict
 
+import matplotlib.scale as mscale
+import matplotlib.transforms as mtransforms
 import numpy as np
+from matplotlib import ticker
 from matplotlib.cbook import normalize_kwargs
 from matplotlib.collections import PathCollection
 from matplotlib.lines import Line2D
@@ -29,6 +33,63 @@ class UnsetDefault:
 unset = UnsetDefault()
 
 
+class SquareRootScale(mscale.ScaleBase):
+    """ScaleBase class for generating square root scale."""
+
+    name = "sqrt"
+
+    def __init__(self, axis, **kwargs):  # pylint: disable=unused-argument
+        mscale.ScaleBase.__init__(self, axis)
+
+    def set_default_locators_and_formatters(self, axis):
+        """Set the locators and formatters to default."""
+        axis.set_major_locator(ticker.AutoLocator())
+        axis.set_major_formatter(ticker.ScalarFormatter())
+        axis.set_minor_locator(ticker.NullLocator())
+        axis.set_minor_formatter(ticker.NullFormatter())
+
+    def limit_range_for_scale(self, vmin, vmax, minpos):  # pylint: disable=unused-argument
+        """Limit the range of the scale."""
+        return max(0.0, vmin), vmax
+
+    class SquareRootTransform(mtransforms.Transform):
+        """Square root transformation."""
+
+        input_dims = 1
+        output_dims = 1
+        is_separable = True
+
+        def transform_non_affine(self, values):
+            """Transform the data."""
+            return np.array(values) ** 0.5
+
+        def inverted(self):
+            """Invert the transformation."""
+            return SquareRootScale.InvertedSquareRootTransform()
+
+    class InvertedSquareRootTransform(mtransforms.Transform):
+        """Inverted square root transformation."""
+
+        input_dims = 1
+        output_dims = 1
+        is_separable = True
+
+        def transform(self, values):
+            """Transform the data."""
+            return np.array(values) ** 2
+
+        def inverted(self):
+            """Invert the transformation."""
+            return SquareRootScale.SquareRootTransform()
+
+    def get_transform(self):
+        """Get the transformation."""
+        return self.SquareRootTransform()
+
+
+mscale.register_scale(SquareRootScale)
+
+
 # generation of default values for aesthetics
 def get_default_aes(aes_key, n, kwargs=None):
     """Generate `n` *matplotlib valid* default values for a given aesthetics keyword."""
@@ -319,6 +380,24 @@ def hline(y, target, *, color=unset, alpha=unset, width=unset, linestyle=unset,
     return target.axhline(y, **_filter_kwargs(kwargs, Line2D, artist_kws))
 
 
+def ciliney(
+    x,
+    y_bottom,
+    y_top,
+    target,
+    *,
+    color=unset,
+    alpha=unset,
+    width=unset,
+    linestyle=unset,
+    **artist_kws,
+):
+    """Interface to matplotlib for a line from y_bottom to y_top at given value of x."""
+    artist_kws.setdefault("zorder", 2)
+    kwargs = {"color": color, "alpha": alpha, "linewidth": width, "linestyle": linestyle}
+    return target.plot([x, x], [y_bottom, y_top], **_filter_kwargs(kwargs, Line2D, artist_kws))[0]
+
+
 # general plot appeareance
 def title(string, target, *, size=unset, color=unset, **artist_kws):
     """Interface to matplotlib for adding a title to a plot."""
@@ -396,3 +475,8 @@ def remove_axis(target, axis="y"):
         target.spines["bottom"].set_visible(False)
     else:
         raise ValueError(f"axis must be one of 'x', 'y' or 'both', got '{axis}'")
+
+
+def set_y_scale(target, scale):
+    """Interface to matplotlib for setting the y scale of a plot."""
+    target.set_yscale(scale)

src/arviz_plots/backend/none/__init__.py

@@ -357,6 +357,33 @@ def hline(y, target, *, color=unset, alpha=unset, width=unset, linestyle=unset,
     return artist_element
 
 
+def ciliney(
+    x,
+    y_bottom,
+    y_top,
+    target,
+    *,
+    color=unset,
+    alpha=unset,
+    width=unset,
+    linestyle=unset,
+    **artist_kws,
+):
+    """Interface to a line from y_bottom to y_top at given value of x."""
+    kwargs = {"color": color, "alpha": alpha, "width": width, "linestyle": linestyle}
+    if not ALLOW_KWARGS and artist_kws:
+        raise ValueError("artist_kws not empty")
+    artist_element = {
+        "function": "line",
+        "x": np.atleast_1d(x),
+        "y_bottom": np.atleast_1d(y_bottom),
+        "y_top": np.atleast_1d(y_top),
+        **_filter_kwargs(kwargs, artist_kws),
+    }
+    target.append(artist_element)
+    return artist_element
+
+
 # general plot appeareance
 def title(string, target, *, size=unset, color=unset, **artist_kws):
     """Interface to adding a title to a plot."""

src/arviz_plots/backend/plotly/__init__.py

@@ -462,6 +462,38 @@ def hline(y, target, *, color=unset, alpha=unset, width=unset, linestyle=unset,
     )
 
 
+def ciliney(
+    x,
+    y_bottom,
+    y_top,
+    target,
+    *,
+    color=unset,
+    alpha=unset,
+    width=unset,
+    linestyle=unset,
+    **artist_kws,
+):
+    """Interface to plotly for a line from y_bottom to y_top at given value of x."""
+    artist_kws.setdefault("showlegend", False)
+    line_kwargs = {"color": color, "width": width, "dash": linestyle}
+    line_artist_kws = artist_kws.pop("line", {}).copy()
+    kwargs = {"opacity": alpha}
+
+    # I was not able to figure it out how to do this withouth a loop
+    # all solutions I tried did not plot the lines or the lines were connected
+    for x_i, y_t, y_b in zip(x, y_top, y_bottom):
+        line_object = go.Scatter(
+            x=[x_i, x_i],
+            y=[y_b, y_t],
+            mode="lines",
+            line=_filter_kwargs(line_kwargs, line_artist_kws),
+            **_filter_kwargs(kwargs, artist_kws),
+        )
+        target.add_trace(line_object)
+    return line_object
+
+
 # general plot appeareance
 def title(string, target, *, size=unset, color=unset, **artist_kws):
     """Interface to plotly for adding a title to a plot."""

src/arviz_plots/plots/__init__.py

@@ -9,6 +9,7 @@
 from .forestplot import plot_forest
 from .pavacalibrationplot import plot_ppc_pava
 from .ppcdistplot import plot_ppc_dist
+from .ppcrootogramplot import plot_ppc_rootogram
 from .psensedistplot import plot_psense_dist
 from .psensequantitiesplot import plot_psense_quantities
 from .ridgeplot import plot_ridge
@@ -26,6 +27,7 @@
     "plot_ess",
     "plot_ess_evolution",
     "plot_ppc_dist",
+    "plot_ppc_rootogram",
     "plot_ridge",
     "plot_ppc_pava",
     "plot_psense_dist",