fixes to matplotlib subplot handling

arviz/plots/backends/matplotlib/pairplot.py

@@ -199,49 +199,52 @@ def plot_pair(
         ax.tick_params(labelsize=xt_labelsize)
 
     else:
+        not_marginals = int(not marginals)
+        num_subplot_cols = numvars - not_marginals
         max_plots = (
-            numvars ** 2 if rcParams["plot.max_subplots"] is None else rcParams["plot.max_subplots"]
+            num_subplot_cols ** 2
+            if rcParams["plot.max_subplots"] is None
+            else rcParams["plot.max_subplots"]
         )
-        vars_to_plot = np.sum(np.arange(numvars).cumsum() < max_plots)
-        if vars_to_plot < numvars:
+        cols_to_plot = np.sum(np.arange(1, num_subplot_cols + 1).cumsum() <= max_plots)
+        if cols_to_plot < num_subplot_cols:
+            vars_to_plot = cols_to_plot
             warnings.warn(
                 "rcParams['plot.max_subplots'] ({max_plots}) is smaller than the number "
                 "of resulting pair plots with these variables, generating only a "
                 "{side}x{side} grid".format(max_plots=max_plots, side=vars_to_plot),
                 UserWarning,
             )
-            numvars = vars_to_plot
+        else:
+            vars_to_plot = numvars - not_marginals
 
         (figsize, ax_labelsize, _, xt_labelsize, _, markersize) = _scale_fig_size(
-            figsize, textsize, numvars - 2, numvars - 2
+            figsize, textsize, vars_to_plot, vars_to_plot
         )
 
         point_estimate_marker_kwargs.setdefault("s", markersize + 50)
 
         if ax is None:
-            fig, ax = plt.subplots(numvars, numvars, figsize=figsize, **backend_kwargs)
+            fig, ax = plt.subplots(vars_to_plot, vars_to_plot, figsize=figsize, **backend_kwargs,)
         hexbin_values = []
-        for i in range(0, numvars):
+        for i in range(0, vars_to_plot):
             var1 = infdata_group[i]
 
-            for j in range(0, numvars):
-                var2 = infdata_group[j]
+            for j in range(0, vars_to_plot):
+                var2 = infdata_group[j + not_marginals]
                 if i > j:
                     if ax[j, i].get_figure() is not None:
                         ax[j, i].remove()
                     continue
 
-                elif i == j:
-                    if marginals:
-                        loc = "right"
-                        plot_dist(var1, ax=ax[i, j], **marginal_kwargs)
-                    else:
-                        loc = "left"
-                        if ax[j, i].get_figure() is not None:
-                            ax[j, i].remove()
-                        continue
+                elif i == j and marginals:
+                    loc = "right"
+                    plot_dist(var1, ax=ax[i, j], **marginal_kwargs)
 
                 else:
+                    if i == j:
+                        loc = "left"
+
                     if "scatter" in kind:
                         ax[j, i].plot(var1, var2, **scatter_kwargs)
 
@@ -285,15 +288,15 @@ def plot_pair(
 
                     if reference_values:
                         x_name = flat_var_names[i]
-                        y_name = flat_var_names[j]
+                        y_name = flat_var_names[j + not_marginals]
                         if x_name and y_name not in difference:
                             ax[j, i].plot(
                                 reference_values_copy[x_name],
                                 reference_values_copy[y_name],
                                 **reference_values_kwargs,
                             )
 
-                if j != numvars - 1:
+                if j != vars_to_plot - 1:
                     ax[j, i].axes.get_xaxis().set_major_formatter(NullFormatter())
                 else:
                     ax[j, i].set_xlabel(
@@ -303,7 +306,9 @@ def plot_pair(
                     ax[j, i].axes.get_yaxis().set_major_formatter(NullFormatter())
                 else:
                     ax[j, i].set_ylabel(
-                        "{}".format(flat_var_names[j]), fontsize=ax_labelsize, wrap=True
+                        "{}".format(flat_var_names[j + not_marginals]),
+                        fontsize=ax_labelsize,
+                        wrap=True,
                     )
                 ax[j, i].tick_params(labelsize=xt_labelsize)
 

arviz/plots/traceplot.py

@@ -230,7 +230,7 @@ def plot_trace(
 
     plotters = list(xarray_var_iter(data, var_names=var_names, combined=True, skip_dims=skip_dims))
     max_plots = rcParams["plot.max_subplots"]
-    max_plots = len(plotters) if max_plots is None else max_plots
+    max_plots = len(plotters) if max_plots is None else max(max_plots // 2, 1)
     if len(plotters) > max_plots:
         warnings.warn(
             "rcParams['plot.max_subplots'] ({max_plots}) is smaller than the number "

arviz/tests/base_tests/test_plots_bokeh.py

@@ -149,7 +149,7 @@ def test_plot_trace_discrete(discrete_model):
 
 def test_plot_trace_max_subplots_warning(models):
     with pytest.warns(UserWarning):
-        with rc_context(rc={"plot.max_subplots": 1}):
+        with rc_context(rc={"plot.max_subplots": 2}):
             axes = plot_trace(models.model_1, backend="bokeh", show=False)
     assert axes.shape
 

arviz/tests/base_tests/test_plots_matplotlib.py

@@ -188,9 +188,9 @@ def test_plot_trace_discrete(discrete_model):
 
 def test_plot_trace_max_subplots_warning(models):
     with pytest.warns(UserWarning):
-        with rc_context(rc={"plot.max_subplots": 1}):
+        with rc_context(rc={"plot.max_subplots": 6}):
             axes = plot_trace(models.model_1)
-    assert axes.shape
+    assert axes.shape == (3, 2)
 
 
 @pytest.mark.parametrize("kwargs", [{"var_names": ["mu", "tau"], "lines": [("hey", {}, [1])]}])
@@ -478,6 +478,21 @@ def test_plot_pair_overlaid(models, kwargs):
     assert ax.shape
 
 
+@pytest.mark.parametrize("marginals", [True, False])
+@pytest.mark.parametrize("max_subplots", [True, False])
+def test_plot_pair_shapes(marginals, max_subplots):
+    rng = np.random.default_rng()
+    idata = from_dict({"a": rng.standard_normal((4, 500, 5))})
+    if max_subplots:
+        with rc_context({"plot.max_subplots": 6}):
+            with pytest.warns(UserWarning, match="3x3 grid"):
+                ax = plot_pair(idata, marginals=marginals)
+    else:
+        ax = plot_pair(idata, marginals=marginals)
+    side = 3 if max_subplots else (4 + marginals)
+    assert ax.shape == (side, side)
+
+
 @pytest.mark.parametrize("kind", ["kde", "cumulative", "scatter"])
 @pytest.mark.parametrize("alpha", [None, 0.2, 1])
 @pytest.mark.parametrize("animated", [False, True])