Khat deprecate annotate in favor of threshold (#1478)

* remove hard limits, show hlines only when show_bins is True * remove hard limits, show hlines only when show_bins is True * update chagelog, revert most changes in bokeh * update tests
arviz-devs · Dec 28, 2020 · 2d202de · 2d202de
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,7 +33,9 @@
 * `plot_elpd`, avoid modifying the input dict ([1477](https://github.com/arviz-devs/arviz/issues/1477))
 * Do not plot divergences in `plot_trace` when `kind=rank_vlines` or `kind=rank_bars` ([1476](https://github.com/arviz-devs/arviz/issues/1476)) 
 
+
 ### Deprecation
+* `plot_khat` deprecate `annotate` argument in favor of `threshold`. The new argument accepts floats ([1478](https://github.com/arviz-devs/arviz/issues/1478))
 
 ### Documentation
 * Reorganize documentation and change sphinx theme ([1406](https://github.com/arviz-devs/arviz/pull/1406))

diff --git a/arviz/plots/backends/bokeh/khatplot.py b/arviz/plots/backends/bokeh/khatplot.py
@@ -21,10 +21,11 @@ def plot_khat(
     xdata,
     khats,
     kwargs,
-    annotate,
+    threshold,
     coord_labels,
+    show_hlines,
     show_bins,
-    hlines_kwargs,  # pylint: disable=unused-argument
+    hlines_kwargs,
     xlabels,  # pylint: disable=unused-argument
     legend,  # pylint: disable=unused-argument
     color,
@@ -49,6 +50,10 @@ def plot_khat(
 
     (figsize, *_, line_width, _) = _scale_fig_size(figsize, textsize)
 
+    if hlines_kwargs is None:
+        hlines_kwargs = {}
+    hlines_kwargs.setdefault("hlines", [0, 0.5, 0.7, 1])
+
     cmap = None
     if isinstance(color, str):
         if color in dims:
@@ -103,21 +108,21 @@ def plot_khat(
             fill_alpha=alphas,
         )
 
-    if annotate:
-        idxs = xdata[khats > 1]
+    if threshold is not None:
+        idxs = xdata[khats > threshold]
         for idx in idxs:
             ax.text(x=[idx], y=[khats[idx]], text=[coord_labels[idx]])
 
-    for hline in [0, 0.5, 0.7, 1]:
-        _hline = Span(
-            location=hline,
-            dimension="width",
-            line_color="grey",
-            line_width=line_width,
-            line_dash="dashed",
-        )
-
-        ax.renderers.append(_hline)
+    if show_hlines:
+        for hline in hlines_kwargs.pop("hlines"):
+            _hline = Span(
+                location=hline,
+                dimension="width",
+                line_color="grey",
+                line_width=line_width,
+                line_dash="dashed",
+            )
+            ax.renderers.append(_hline)
 
     ymin = min(khats)
     ymax = max(khats)
@@ -134,14 +139,15 @@ def plot_khat(
                 text=[bin_format.format(count, count / n_data_points * 100)],
             )
         ax.x_range._property_values["end"] = xmax + 1  # pylint: disable=protected-access
+
     ax.xaxis.axis_label = "Data Point"
     ax.yaxis.axis_label = "Shape parameter k"
 
     if ymin > 0:
         ax.y_range._property_values["start"] = -0.02  # pylint: disable=protected-access
     if ymax < 1:
         ax.y_range._property_values["end"] = 1.02  # pylint: disable=protected-access
-    elif ymax > 1 & annotate:
+    elif ymax > 1 & threshold:
         ax.y_range._property_values["end"] = 1.1 * ymax  # pylint: disable=protected-access
 
     show_layout(ax, show)

diff --git a/arviz/plots/backends/matplotlib/khatplot.py b/arviz/plots/backends/matplotlib/khatplot.py
@@ -20,8 +20,9 @@ def plot_khat(
     xdata,
     khats,
     kwargs,
-    annotate,
+    threshold,
     coord_labels,
+    show_hlines,
     show_bins,
     hlines_kwargs,
     xlabels,
@@ -61,6 +62,7 @@ def plot_khat(
     backend_kwargs["squeeze"] = True
 
     hlines_kwargs = matplotlib_kwarg_dealiaser(hlines_kwargs, "hlines")
+    hlines_kwargs.setdefault("hlines", [0, 0.5, 0.7, 1])
     hlines_kwargs.setdefault("linestyle", [":", "-.", "--", "-"])
     hlines_kwargs.setdefault("alpha", 0.7)
     hlines_kwargs.setdefault("zorder", -1)
@@ -109,8 +111,8 @@ def plot_khat(
 
     sc_plot = ax.scatter(xdata, khats, c=rgba_c, **kwargs)
 
-    if annotate:
-        idxs = xdata[khats > 1]
+    if threshold is not None:
+        idxs = xdata[khats > threshold]
         for idx in idxs:
             ax.text(
                 idx,
@@ -125,10 +127,15 @@ def plot_khat(
     if show_bins:
         xmax += n_data_points / 12
     ylims1 = ax.get_ylim()
-    ax.hlines([0, 0.5, 0.7, 1], xmin=xmin, xmax=xmax, linewidth=linewidth, **hlines_kwargs)
     ylims2 = ax.get_ylim()
     ymin = min(ylims1[0], ylims2[0])
     ymax = min(ylims1[1], ylims2[1])
+
+    if show_hlines:
+        ax.hlines(
+            hlines_kwargs.pop("hlines"), xmin=xmin, xmax=xmax, linewidth=linewidth, **hlines_kwargs
+        )
+
     if show_bins:
         bin_edges = np.array([ymin, 0.5, 0.7, 1, ymax])
         bin_edges = bin_edges[(bin_edges >= ymin) & (bin_edges <= ymax)]
@@ -141,8 +148,6 @@ def plot_khat(
                 horizontalalignment="center",
                 verticalalignment="center",
             )
-    ax.set_ylim(ymin, ymax)
-    ax.set_xlim(xmin, xmax)
 
     ax.set_xlabel("Data Point", fontsize=ax_labelsize)
     ax.set_ylabel(r"Shape parameter k", fontsize=ax_labelsize)

diff --git a/arviz/plots/khatplot.py b/arviz/plots/khatplot.py
@@ -1,4 +1,6 @@
 """Pareto tail indices plot."""
+import logging
+
 import numpy as np
 from xarray import DataArray
 
@@ -7,14 +9,18 @@
 from ..utils import get_coords
 from .plot_utils import format_coords_as_labels, get_plotting_function
 
+_log = logging.getLogger(__name__)
+
 
 def plot_khat(
     khats,
     color="C0",
     xlabels=False,
+    show_hlines=False,
     show_bins=False,
     bin_format="{1:.1f}%",
     annotate=False,
+    threshold=None,
     hover_label=False,
     hover_format="{1}",
     figsize=None,
@@ -42,12 +48,15 @@ def plot_khat(
         otherwise, it will be interpreted as a list of the dims to be used for the color code
     xlabels : bool, optional
         Use coords as xticklabels
+    show_hlines : bool, optional
+        Show the horizontal lines, by default at the values [0, 0.5, 0.7, 1].
     show_bins : bool, optional
-        Show the number of khats which fall in each bin.
+        Show the percentage of khats falling in each bin, as delimited by hlines.
     bin_format : str, optional
         The string is used as formatting guide calling ``bin_format.format(count, pct)``.
-    annotate : bool, optional
-        Show the labels of k values larger than 1.
+    threshold : float, optional
+        Show the labels of k values larger than threshold. Defaults to `None`,
+        no observations will be highlighted.
     hover_label : bool, optional
         Show the datapoint label when hovering over it with the mouse. Requires an interactive
         backend.
@@ -103,7 +112,7 @@ def plot_khat(
 
         >>> centered_eight = az.load_arviz_data("centered_eight")
         >>> khats = az.loo(centered_eight, pointwise=True).pareto_k
-        >>> az.plot_khat(khats, xlabels=True, annotate=True)
+        >>> az.plot_khat(khats, xlabels=True, threshold=1)
 
     Use custom color scheme
 
@@ -117,6 +126,10 @@ def plot_khat(
         >>> az.plot_khat(loo_radon, color=colors)
 
     """
+    if annotate:
+        _log.warning("annotate will be deprecated, please use threshold instead")
+        threshold = annotate
+
     if coords is None:
         coords = {}
 
@@ -152,8 +165,9 @@ def plot_khat(
         xdata=xdata,
         khats=khats,
         kwargs=kwargs,
-        annotate=annotate,
+        threshold=threshold,
         coord_labels=coord_labels,
+        show_hlines=show_hlines,
         show_bins=show_bins,
         hlines_kwargs=hlines_kwargs,
         xlabels=xlabels,

diff --git a/arviz/tests/base_tests/test_plots_bokeh.py b/arviz/tests/base_tests/test_plots_bokeh.py
@@ -601,7 +601,12 @@ def test_plot_joint_bad(models):
         {"color": "obs_dim", "legend": True, "hover_label": True},
         {"color": "blue", "coords": {"obs_dim": slice(2, 4)}},
         {"color": np.random.uniform(size=8), "show_bins": True},
-        {"color": np.random.uniform(size=(8, 3)), "show_bins": True, "annotate": True},
+        {
+            "color": np.random.uniform(size=(8, 3)),
+            "show_bins": True,
+            "show_hlines": True,
+            "threshold": 1,
+        },
     ],
 )
 @pytest.mark.parametrize("input_type", ["elpd_data", "data_array", "array"])
@@ -628,7 +633,12 @@ def test_plot_khat(models, input_type, kwargs):
         {"color": "dim2", "legend": True, "hover_label": True},
         {"color": "blue", "coords": {"dim2": slice(2, 4)}},
         {"color": np.random.uniform(size=35), "show_bins": True},
-        {"color": np.random.uniform(size=(35, 3)), "show_bins": True, "annotate": True},
+        {
+            "color": np.random.uniform(size=(35, 3)),
+            "show_bins": True,
+            "show_hlines": True,
+            "threshold": 1,
+        },
     ],
 )
 @pytest.mark.parametrize("input_type", ["elpd_data", "data_array", "array"])
@@ -650,9 +660,9 @@ def test_plot_khat_multidim(multidim_models, input_type, kwargs):
     assert axes
 
 
-def test_plot_khat_annotate():
+def test_plot_khat_threshold():
     khats = np.array([0, 0, 0.6, 0.6, 0.8, 0.9, 0.9, 2, 3, 4, 1.5])
-    axes = plot_khat(khats, annotate=True, backend="bokeh", show=False)
+    axes = plot_khat(khats, threshold=1, backend="bokeh", show=False)
     assert axes
 
 

diff --git a/arviz/tests/base_tests/test_plots_matplotlib.py b/arviz/tests/base_tests/test_plots_matplotlib.py
@@ -1138,7 +1138,12 @@ def test_plot_elpd_one_model(models):
         {"color": "obs_dim", "legend": True, "hover_label": True},
         {"color": "blue", "coords": {"obs_dim": slice(2, 4)}},
         {"color": np.random.uniform(size=8), "show_bins": True},
-        {"color": np.random.uniform(size=(8, 3)), "show_bins": True, "annotate": True},
+        {
+            "color": np.random.uniform(size=(8, 3)),
+            "show_bins": True,
+            "show_hlines": True,
+            "threshold": 1,
+        },
     ],
 )
 @pytest.mark.parametrize("input_type", ["elpd_data", "data_array", "array"])
@@ -1165,7 +1170,12 @@ def test_plot_khat(models, input_type, kwargs):
         {"color": "dim2", "legend": True, "hover_label": True},
         {"color": "blue", "coords": {"dim2": slice(2, 4)}},
         {"color": np.random.uniform(size=35), "show_bins": True},
-        {"color": np.random.uniform(size=(35, 3)), "show_bins": True, "annotate": True},
+        {
+            "color": np.random.uniform(size=(35, 3)),
+            "show_bins": True,
+            "show_hlines": True,
+            "threshold": 1,
+        },
     ],
 )
 @pytest.mark.parametrize("input_type", ["elpd_data", "data_array", "array"])
@@ -1187,9 +1197,9 @@ def test_plot_khat_multidim(multidim_models, input_type, kwargs):
     assert axes
 
 
-def test_plot_khat_annotate():
+def test_plot_khat_threshold():
     khats = np.array([0, 0, 0.6, 0.6, 0.8, 0.9, 0.9, 2, 3, 4, 1.5])
-    axes = plot_khat(khats, annotate=True)
+    axes = plot_khat(khats, threshold=1)
     assert axes