improve plots + plot posterior mu rather than posterior predictive

Author: drbenvincent

causalpy/plot_utils.py

@@ -5,6 +5,7 @@
 import numpy as np
 import pandas as pd
 import xarray as xr
+from matplotlib.collections import PolyCollection
 
 
 def plot_xY(
@@ -13,28 +14,46 @@ def plot_xY(
     ax: plt.Axes,
     plot_hdi_kwargs: Optional[Dict[str, Any]] = None,
     hdi_prob: float = 0.94,
+    label: Optional[str] = "",
     include_label: bool = True,
-) -> None:
+):
     """Utility function to plot HDI intervals."""
 
     if plot_hdi_kwargs is None:
         plot_hdi_kwargs = {}
 
-    az.plot_hdi(
+    (h_line,) = ax.plot(
+        x,
+        Y.mean(dim=["chain", "draw"]),
+        ls="-",
+        **plot_hdi_kwargs,
+        label=f"{label}" if include_label else None,
+    )
+    ax_hdi = az.plot_hdi(
         x,
         Y,
         hdi_prob=hdi_prob,
         fill_kwargs={
             "alpha": 0.25,
-            "label": f"{hdi_prob*100}% HDI" if include_label else None,
+            "label": " ",  # f"{hdi_prob*100}% HDI" if include_label else None,
         },
         smooth=False,
         ax=ax,
         **plot_hdi_kwargs,
     )
-    ax.plot(
-        x,
-        Y.mean(dim=["chain", "draw"]),
-        color="k",
-        label="Posterior mean" if include_label else None,
-    )
+    # Return handle to patch.
+    # We get a list of the childen of the axis
+    # Filter for just the PolyCollection objects
+    # Take the last one
+    h_patch = list(
+        filter(lambda x: isinstance(x, PolyCollection), ax_hdi.get_children())
+    )[-1]
+
+    # if include_label:
+    #     handles, labels = ax.get_legend_handles_labels()
+    #     ax.legend(
+    #         handles=[(h1, h2) for h1, h2 in zip(handles[::2], handles[1::2])],
+    #         # labels=[l1 + " + " + l2 for l1, l2 in zip(labels[::2], labels[1::2])],
+    #         labels=[l1 for l1 in labels[::2]],
+    #     )
+    return h_line, h_patch

causalpy/pymc_experiments.py

@@ -99,13 +99,13 @@ def __init__(
         # causal impact pre (ie the residuals of the model fit to observed)
         pre_data = xr.DataArray(self.pre_y[:, 0], dims=["obs_ind"])
         self.pre_impact = (
-            pre_data - self.pre_pred["posterior_predictive"].y_hat
+            pre_data - self.pre_pred["posterior_predictive"].mu
         ).transpose(..., "obs_ind")
 
         # causal impact post (ie the residuals of the model fit to observed)
         post_data = xr.DataArray(self.post_y[:, 0], dims=["obs_ind"])
         self.post_impact = (
-            post_data - self.post_pred["posterior_predictive"].y_hat
+            post_data - self.post_pred["posterior_predictive"].mu
         ).transpose(..., "obs_ind")
 
         # cumulative impact post
@@ -118,31 +118,47 @@ def plot(self):
 
         # TOP PLOT --------------------------------------------------
         # pre-intervention period
-        plot_xY(
+        h_line, h_patch = plot_xY(
             self.datapre.index,
-            self.pre_pred["posterior_predictive"].y_hat,
+            self.pre_pred["posterior_predictive"].mu,
             ax=ax[0],
+            include_label=False,
+            plot_hdi_kwargs={"color": "C0"},
         )
-        ax[0].plot(self.datapre.index, self.pre_y, "k.", label="Observations")
+        handles = [(h_line, h_patch)]
+        labels = ["Pre-intervention period"]
+
+        (h,) = ax[0].plot(self.datapre.index, self.pre_y, "k.", label="Observations")
+        handles.append(h)
+        labels.append("Observations")
+
         # post intervention period
-        plot_xY(
+        h_line, h_patch = plot_xY(
             self.datapost.index,
-            self.post_pred["posterior_predictive"].y_hat,
+            self.post_pred["posterior_predictive"].mu,
             ax=ax[0],
             include_label=False,
+            # label="Synthetic control",
+            plot_hdi_kwargs={"color": "C1"},
         )
+        handles.append((h_line, h_patch))
+        labels.append("Synthetic control")
+
         ax[0].plot(self.datapost.index, self.post_y, "k.")
         # Shaded causal effect
-        ax[0].fill_between(
+        h = ax[0].fill_between(
             self.datapost.index,
             y1=az.extract(
-                self.post_pred, group="posterior_predictive", var_names="y_hat"
+                self.post_pred, group="posterior_predictive", var_names="mu"
             ).mean("sample"),
             y2=np.squeeze(self.post_y),
-            color="C0",
+            color="C2",
             alpha=0.25,
-            label="Causal impact",
+            # label="Causal impact",
         )
+        handles.append(h)
+        labels.append("Causal impact")
+
         ax[0].set(
             title=f"""
             Pre-intervention Bayesian $R^2$: {self.score.r2:.3f}
@@ -155,30 +171,34 @@ def plot(self):
             self.datapre.index,
             self.pre_impact,
             ax=ax[1],
+            include_label=False,
+            plot_hdi_kwargs={"color": "C0"},
         )
         plot_xY(
             self.datapost.index,
             self.post_impact,
             ax=ax[1],
             include_label=False,
+            plot_hdi_kwargs={"color": "C1"},
         )
         ax[1].axhline(y=0, c="k")
         ax[1].fill_between(
             self.datapost.index,
             y1=self.post_impact.mean(["chain", "draw"]),
-            color="C0",
+            color="C2",
             alpha=0.25,
             label="Causal impact",
         )
         ax[1].set(title="Causal Impact")
 
         # BOTTOM PLOT -----------------------------------------------
-
         ax[2].set(title="Cumulative Causal Impact")
         plot_xY(
             self.datapost.index,
             self.post_impact_cumulative,
             ax=ax[2],
+            include_label=False,
+            plot_hdi_kwargs={"color": "C1"},
         )
         ax[2].axhline(y=0, c="k")
 
@@ -189,10 +209,14 @@ def plot(self):
                 ls="-",
                 lw=3,
                 color="r",
-                label="Treatment time",
+                # label="Treatment time",
             )
 
-        ax[0].legend(fontsize=LEGEND_FONT_SIZE)
+        ax[0].legend(
+            handles=(h_tuple for h_tuple in handles),
+            labels=labels,
+            fontsize=LEGEND_FONT_SIZE,
+        )
 
         return (fig, ax)
 
@@ -353,39 +377,46 @@ def __init__(
         )
 
     def plot(self):
-        """Plot the results"""
+        """Plot the results.
+        Creating the combined mean + HDI legend entries is a bit involved.
+        """
         fig, ax = plt.subplots()
 
         # Plot raw data
-        # NOTE: This will not work when there is just ONE unit in each group
-        sns.lineplot(
+        sns.scatterplot(
             self.data,
             x=self.time_variable_name,
             y=self.outcome_variable_name,
             hue=self.group_variable_name,
-            units="unit",  # NOTE: assumes we have a `unit` predictor variable
-            estimator=None,
-            alpha=0.5,
+            alpha=1,
+            legend=False,
+            markers=True,
             ax=ax,
         )
 
         # Plot model fit to control group
         time_points = self.x_pred_control[self.time_variable_name].values
-        plot_xY(
+        h_line, h_patch = plot_xY(
             time_points,
-            self.y_pred_control.posterior_predictive.y_hat,
+            self.y_pred_control.posterior_predictive.mu,
             ax=ax,
             plot_hdi_kwargs={"color": "C0"},
+            label="Control group",
         )
+        handles = [(h_line, h_patch)]
+        labels = ["Control group"]
 
         # Plot model fit to treatment group
         time_points = self.x_pred_control[self.time_variable_name].values
-        plot_xY(
+        h_line, h_patch = plot_xY(
             time_points,
-            self.y_pred_treatment.posterior_predictive.y_hat,
+            self.y_pred_treatment.posterior_predictive.mu,
             ax=ax,
             plot_hdi_kwargs={"color": "C1"},
+            label="Treatment group",
         )
+        handles.append((h_line, h_patch))
+        labels.append("Treatment group")
 
         # Plot counterfactual - post-test for treatment group IF no treatment
         # had occurred.
@@ -407,22 +438,30 @@ def plot(self):
                 pc.set_edgecolor("None")
                 pc.set_alpha(0.5)
         else:
-            plot_xY(
+            h_line, h_patch = plot_xY(
                 time_points,
-                self.y_pred_counterfactual.posterior_predictive.y_hat,
+                self.y_pred_counterfactual.posterior_predictive.mu,
                 ax=ax,
                 plot_hdi_kwargs={"color": "C2"},
+                label="Counterfactual",
             )
+            handles.append((h_line, h_patch))
+            labels.append("Counterfactual")
 
         # arrow to label the causal impact
         self._plot_causal_impact_arrow(ax)
+
         # formatting
         ax.set(
             xticks=self.x_pred_treatment[self.time_variable_name].values,
             title=self._causal_impact_summary_stat(),
         )
-        ax.legend(fontsize=LEGEND_FONT_SIZE)
-        return (fig, ax)
+        ax.legend(
+            handles=(h_tuple for h_tuple in handles),
+            labels=labels,
+            fontsize=LEGEND_FONT_SIZE,
+        )
+        return fig, ax
 
     def _plot_causal_impact_arrow(self, ax):
         """
@@ -582,12 +621,17 @@ def plot(self):
             c="k",  # hue="treated",
             ax=ax,
         )
+
         # Plot model fit to data
-        plot_xY(
+        h_line, h_patch = plot_xY(
             self.x_pred[self.running_variable_name],
             self.pred["posterior_predictive"].mu,
             ax=ax,
+            plot_hdi_kwargs={"color": "C1"},
         )
+        handles = [(h_line, h_patch)]
+        labels = ["Posterior mean"]
+
         # create strings to compose title
         title_info = f"{self.score.r2:.3f} (std = {self.score.r2_std:.3f})"
         r2 = f"Bayesian $R^2$ on all data = {title_info}"
@@ -605,7 +649,11 @@ def plot(self):
             color="r",
             label="treatment threshold",
         )
-        ax.legend(fontsize=LEGEND_FONT_SIZE)
+        ax.legend(
+            handles=(h_tuple for h_tuple in handles),
+            labels=labels,
+            fontsize=LEGEND_FONT_SIZE,
+        )
         return (fig, ax)
 
     def summary(self):
@@ -710,27 +758,38 @@ def plot(self):
             hue="group",
             alpha=0.5,
             data=self.data,
+            legend=True,
             ax=ax[0],
         )
         ax[0].set(xlabel="Pretest", ylabel="Posttest")
 
         # plot posterior predictive of untreated
-        plot_xY(
+        h_line, h_patch = plot_xY(
             self.pred_xi,
-            self.pred_untreated["posterior_predictive"].y_hat,
+            self.pred_untreated["posterior_predictive"].mu,
             ax=ax[0],
             plot_hdi_kwargs={"color": "C0"},
+            label="Control group",
         )
+        handles = [(h_line, h_patch)]
+        labels = ["Control group"]
 
         # plot posterior predictive of treated
-        plot_xY(
+        h_line, h_patch = plot_xY(
             self.pred_xi,
-            self.pred_treated["posterior_predictive"].y_hat,
+            self.pred_treated["posterior_predictive"].mu,
             ax=ax[0],
             plot_hdi_kwargs={"color": "C1"},
+            label="Treatment group",
         )
+        handles.append((h_line, h_patch))
+        labels.append("Treatment group")
 
-        ax[0].legend(fontsize=LEGEND_FONT_SIZE)
+        ax[0].legend(
+            handles=(h_tuple for h_tuple in handles),
+            labels=labels,
+            fontsize=LEGEND_FONT_SIZE,
+        )
 
         # Plot estimated caual impact / treatment effect
         az.plot_posterior(self.causal_impact, ref_val=0, ax=ax[1])