Add layout properties for Bokeh backend.

CHANGELOG.md

@@ -21,6 +21,7 @@
 * **Experimental Feature**: Added `reloo` function to ArviZ
 * ArviZ version to InferenceData attributes. (#1086)
 * Add `log_likelihood` argument to `from_pymc3`
+* Integrated rcParams for `plot.bokeh.layout` and `plot.backend`. (#1089)
 
 
 ### Maintenance and fixes

arviz/plots/autocorrplot.py

@@ -7,6 +7,7 @@
     filter_plotters_list,
     get_plotting_function,
 )
+from ..rcparams import rcParams
 from ..utils import _var_names
 
 
@@ -127,6 +128,10 @@ def plot_autocorr(
         show=show,
     )
 
+    if backend is None:
+        backend = rcParams["plot.backend"]
+    backend = backend.lower()
+
     if backend == "bokeh":
 
         autocorr_plot_args.pop("xt_labelsize")

arviz/plots/backends/__init__.py

@@ -1,7 +1,11 @@
 # pylint: disable=no-member,invalid-name,redefined-outer-name
 """ArviZ plotting backends."""
+import re
+import numpy as np
 from pandas import DataFrame
 
+from ...rcparams import rcParams
+
 
 def to_cds(
     data,
@@ -102,6 +106,76 @@ def ColumnDataSource(*args, **kwargs):
     return ColumnDataSource(*args, **kwargs)
 
 
+def create_layout(ax, force_layout=False):
+    """Transform bokeh array of figures to layout."""
+    ax = np.atleast_2d(ax)
+    subplot_order = rcParams["plot.bokeh.layout.order"]
+    if force_layout:
+        from bokeh.layouts import gridplot as layout
+
+        ax = ax.tolist()
+        layout_args = {
+            "sizing_mode": rcParams["plot.bokeh.layout.sizing_mode"],
+            "toolbar_location": rcParams["plot.bokeh.layout.toolbar_location"],
+        }
+    elif any(item in subplot_order for item in ("row", "column")):
+        # check number of rows
+        match = re.match(r"(\d*)(row|column)", subplot_order)
+        n = int(match.group(1)) if match.group(1) is not None else 1
+        subplot_order = match.group(2)
+        # set up 1D list of axes
+        ax = [item for item in ax.ravel().tolist() if item is not None]
+        layout_args = {"sizing_mode": rcParams["plot.bokeh.layout.sizing_mode"]}
+        if subplot_order == "row" and n == 1:
+            from bokeh.layouts import row as layout
+        elif subplot_order == "column" and n == 1:
+            from bokeh.layouts import column as layout
+        else:
+            from bokeh.layouts import layout
+
+        if n != 1:
+            ax = np.array(ax + [None for _ in range(int(np.ceil(len(ax) / n)) - len(ax))])
+            if subplot_order == "row":
+                ax = ax.reshape(n, -1)
+            else:
+                ax = ax.reshape(-1, n)
+            ax = ax.tolist()
+    else:
+        if subplot_order in ("square", "square_trimmed"):
+            ax = [item for item in ax.ravel().tolist() if item is not None]
+            n = int(np.ceil(len(ax) ** 0.5))
+            ax = ax + [None for _ in range(n ** 2 - len(ax))]
+            ax = np.array(ax).reshape(n, n)
+        ax = ax.tolist()
+        if (subplot_order == "square_trimmed") and any(
+            all(item is None for item in row) for row in ax
+        ):
+            from bokeh.layouts import layout
+
+            ax = [row for row in ax if not all(item is None for item in row)]
+            layout_args = {"sizing_mode": rcParams["plot.bokeh.layout.sizing_mode"]}
+        else:
+            from bokeh.layouts import gridplot as layout
+
+            layout_args = {
+                "sizing_mode": rcParams["plot.bokeh.layout.sizing_mode"],
+                "toolbar_location": rcParams["plot.bokeh.layout.toolbar_location"],
+            }
+
+    return layout(ax, **layout_args)
+
+
+def show_layout(ax, show=True, force_layout=False):
+    """Create a layout and call bokeh show."""
+    if show is None:
+        show = rcParams["plot.bokeh.show"]
+    if show:
+        import bokeh.plotting as bkp
+
+        layout = create_layout(ax, force_layout=force_layout)
+        bkp.show(layout)
+
+
 def _copy_docstring(lib, function):
     """Extract docstring from function."""
     import importlib

arviz/plots/backends/bokeh/__init__.py

@@ -1,6 +1,7 @@
 # pylint: disable=wrong-import-position
 """Bokeh Plotting Backend."""
 from packaging import version
+from ....rcparams import rcParams
 
 
 def backend_kwarg_defaults(*args, **kwargs):
@@ -12,14 +13,19 @@ def backend_kwarg_defaults(*args, **kwargs):
     # add needed default args from arviz.rcParams
     for key, arg in args:
         defaults.setdefault(key, rcParams[arg])
-    return defaults
-
 
-def backend_show(show):
-    """Set default behaviour for show if not explicitly defined."""
-    if show is None:
-        show = rcParams["plot.bokeh.show"]
-    return show
+    for key, arg in {
+        "toolbar_location": "plot.bokeh.layout.toolbar_location",
+        "tools": "plot.bokeh.tools",
+        "output_backend": "plot.bokeh.output_backend",
+        "height": "plot.bokeh.figure.height",
+        "width": "plot.bokeh.figure.width",
+    }.items():
+        # by default, ignore height and width if dpi is used
+        if key in ("height", "width") and "dpi" in defaults:
+            continue
+        defaults.setdefault(key, rcParams[arg])
+    return defaults
 
 
 from .autocorrplot import plot_autocorr
@@ -43,7 +49,6 @@ def backend_show(show):
 from .rankplot import plot_rank
 from .traceplot import plot_trace
 from .violinplot import plot_violin
-from ....rcparams import rcParams
 
 
 def check_bokeh_version():

arviz/plots/backends/bokeh/autocorrplot.py

@@ -1,11 +1,10 @@
 """Bokeh Autocorrplot."""
-import bokeh.plotting as bkp
-import numpy as np
-from bokeh.layouts import gridplot
 from bokeh.models import DataRange1d
 from bokeh.models.annotations import Title
+import numpy as np
 
-from . import backend_kwarg_defaults, backend_show
+from . import backend_kwarg_defaults
+from .. import show_layout
 from ...plot_utils import _create_axes_grid, make_label
 from ....stats import autocorr
 
@@ -39,7 +38,7 @@ def plot_autocorr(
         backend_kwargs = {}
 
     backend_kwargs = {
-        **backend_kwarg_defaults(),
+        **backend_kwarg_defaults(("dpi", "plot.bokeh.figure.dpi"),),
         **backend_kwargs,
     }
 
@@ -89,6 +88,6 @@ def plot_autocorr(
         ax.x_range = data_range_x
         ax.y_range = data_range_y
 
-    if backend_show(show):
-        bkp.show(gridplot(axes.tolist(), toolbar_location="above"))
+    show_layout(axes, show)
+
     return axes

arviz/plots/backends/bokeh/compareplot.py

@@ -2,7 +2,8 @@
 import bokeh.plotting as bkp
 from bokeh.models import Span
 
-from . import backend_kwarg_defaults, backend_show
+from . import backend_kwarg_defaults
+from .. import show_layout
 
 
 def plot_compare(
@@ -26,17 +27,15 @@ def plot_compare(
         backend_kwargs = {}
 
     backend_kwargs = {
-        **backend_kwarg_defaults(
-            ("tools", "plot.bokeh.tools"),
-            ("output_backend", "plot.bokeh.output_backend"),
-            ("dpi", "plot.bokeh.figure.dpi"),
-        ),
+        **backend_kwarg_defaults(("dpi", "plot.bokeh.figure.dpi"),),
         **backend_kwargs,
     }
     dpi = backend_kwargs.pop("dpi")
 
     if ax is None:
-        ax = bkp.figure(width=figsize[0] * dpi, height=figsize[1] * dpi, **backend_kwargs)
+        backend_kwargs.setdefault("width", int(figsize[0] * dpi))
+        backend_kwargs.setdefault("height", int(figsize[1] * dpi))
+        ax = bkp.figure(**backend_kwargs)
 
     yticks_pos = list(yticks_pos)
 
@@ -130,7 +129,6 @@ def plot_compare(
     ax.y_range._property_values["start"] = -1 + step  # pylint: disable=protected-access
     ax.y_range._property_values["end"] = 0 - step  # pylint: disable=protected-access
 
-    if backend_show(show):
-        bkp.show(ax, toolbar_location="above")
+    show_layout(ax, show)
 
     return ax

arviz/plots/backends/bokeh/densityplot.py

@@ -1,11 +1,11 @@
 """Bokeh Densityplot."""
 from collections import defaultdict
-import numpy as np
-import bokeh.plotting as bkp
-from bokeh.layouts import gridplot
+
 from bokeh.models.annotations import Title, Legend
+import numpy as np
 
-from . import backend_kwarg_defaults, backend_show
+from . import backend_kwarg_defaults
+from .. import show_layout
 from ...plot_utils import (
     make_label,
     _create_axes_grid,
@@ -43,7 +43,7 @@ def plot_density(
         backend_kwargs = {}
 
     backend_kwargs = {
-        **backend_kwarg_defaults(),
+        **backend_kwarg_defaults(("dpi", "plot.bokeh.figure.dpi"),),
         **backend_kwargs,
     }
 
@@ -99,9 +99,7 @@ def plot_density(
         ax1.add_layout(legend, "above")
         ax1.legend.click_policy = "hide"
 
-    if backend_show(show):
-        grid = gridplot(ax.tolist(), toolbar_location="above")
-        bkp.show(grid)
+    show_layout(ax, show)
 
     return ax
 

arviz/plots/backends/bokeh/distplot.py

@@ -2,7 +2,8 @@
 import bokeh.plotting as bkp
 import numpy as np
 
-from . import backend_kwarg_defaults, backend_show
+from . import backend_kwarg_defaults
+from .. import show_layout
 from ...kdeplot import plot_kde
 from ...plot_utils import get_bins
 
@@ -37,12 +38,7 @@ def plot_dist(
         backend_kwargs = {}
 
     backend_kwargs = {
-        **backend_kwarg_defaults(
-            ("tools", "plot.bokeh.tools"),
-            ("output_backend", "plot.bokeh.output_backend"),
-            ("width", "plot.bokeh.figure.width"),
-            ("height", "plot.bokeh.figure.height"),
-        ),
+        **backend_kwarg_defaults(),
         **backend_kwargs,
     }
     if ax is None:
@@ -88,8 +84,8 @@ def plot_dist(
     else:
         raise TypeError('Invalid "kind":{}. Select from {{"auto","kde","hist"}}'.format(kind))
 
-    if backend_show(show):
-        bkp.show(ax, toolbar_location="above")
+    show_layout(ax, show)
+
     return ax
 
 

arviz/plots/backends/bokeh/elpdplot.py

@@ -2,13 +2,13 @@
 import warnings
 
 import bokeh.plotting as bkp
-import numpy as np
-from bokeh.layouts import gridplot
 from bokeh.models.annotations import Title
 from bokeh.models import ColumnDataSource
 import bokeh.models.markers as mk
+import numpy as np
 
-from . import backend_kwarg_defaults, backend_show
+from . import backend_kwarg_defaults
+from .. import show_layout
 from ...plot_utils import _scale_fig_size
 from ....rcparams import rcParams, _validate_bokeh_marker
 
@@ -34,11 +34,7 @@ def plot_elpd(
         backend_kwargs = {}
 
     backend_kwargs = {
-        **backend_kwarg_defaults(
-            ("tools", "plot.bokeh.tools"),
-            ("output_backend", "plot.bokeh.output_backend"),
-            ("dpi", "plot.bokeh.figure.dpi"),
-        ),
+        **backend_kwarg_defaults(("dpi", "plot.bokeh.figure.dpi"),),
         **backend_kwargs,
     }
     dpi = backend_kwargs.pop("dpi")
@@ -49,16 +45,15 @@ def plot_elpd(
         plot_kwargs.setdefault("s", markersize)
 
         if ax is None:
-            ax = bkp.figure(
-                width=int(figsize[0] * dpi), height=int(figsize[1] * dpi), **backend_kwargs
-            )
+            backend_kwargs.setdefault("width", int(figsize[0] * dpi))
+            backend_kwargs.setdefault("height", int(figsize[1] * dpi))
+            ax = bkp.figure(**backend_kwargs)
         ydata = pointwise_data[0] - pointwise_data[1]
         _plot_atomic_elpd(
             ax, xdata, ydata, *models, threshold, coord_labels, xlabels, True, True, plot_kwargs
         )
 
-        if backend_show(show):
-            bkp.show(ax, toolbar_location="above")
+        show_layout(ax, show)
 
     else:
         max_plots = (
@@ -129,8 +124,8 @@ def plot_elpd(
                     plot_kwargs,
                 )
 
-        if backend_show(show):
-            bkp.show(gridplot(ax.tolist(), toolbar_location="above"))
+        show_layout(ax, show)
+
     return ax