barplots for global sensitivity

Author: matthiaskoenig

src/sbmlsim/sensitivity/analysis.py

@@ -26,7 +26,7 @@
 
 from sbmlsim.sensitivity.parameters import SensitivityParameter
 from sbmlsim.sensitivity.outputs import SensitivityOutput
-from sbmlsim.sensitivity.plots import heatmap
+from sbmlsim.sensitivity.plots import heatmap, sobol_barplot
 
 
 class SensitivitySimulation:
@@ -487,23 +487,40 @@ def calculate_sensitivity(self) -> None:
     def plot_sobol_indices(
         self,
         fig_path: Path,
+        **kwargs
         ):
         """Barplots for the Sobol indices.
 
         """
-        parameter_labels: dict[str, str] = {p.uid: f"{p.uid}: {p.name}" for p in self.parameters}
+        # parameter_labels: dict[str, str] = {p.uid: f"{p.uid}: {p.name}" for p in self.parameters}
+        parameter_labels: dict[str, str] = {p.uid: p.uid for p in self.parameters}
         output_labels: dict[str, str] = {q.uid: q.name for q in self.outputs}
 
+        ymax = self.sensitivity["ST"].max(dim=None)
+        ymin = self.sensitivity["S1"].min(dim=None)
+        console.print(f"{ymax=}")
 
         for ko, output in enumerate(self.outputs):
+            f_path = fig_path.parent / f"{fig_path.stem}_{output.uid}{fig_path.suffix}"
+
             S1 = self.sensitivity["S1"][:, ko]
             ST = self.sensitivity["ST"][:, ko]
             S1_conf = self.sensitivity["S1_conf"][:, ko]
             ST_conf = self.sensitivity["ST_conf"][:, ko]
             console.print(S1)
             console.print(type(S1))
+            sobol_barplot(
+                S1=S1,
+                ST=ST,
+                S1_conf=S1_conf,
+                ST_conf=ST_conf,
+                title=output_labels[output.uid],
+                fig_path=f_path,
+                parameter_labels=parameter_labels,
+                ymax=np.max([1.05, ymax]),
+                ymin=np.min([-0.05, ymin]),
+            )
 
-            break
 
 
 

src/sbmlsim/sensitivity/plots.py

@@ -117,5 +117,44 @@ def calculate_subset(df, cutoff=0.01) -> pd.DataFrame:
     plt.show()
 
 
-def sobol_barplot():
-    pass
+def sobol_barplot(
+    S1, ST, S1_conf, ST_conf,
+    parameter_labels: dict[str, str],
+    fig_path: Optional[Path] = None,
+    title: Optional[str] = None,
+    ymax: float = 1.1,
+    ymin: float = -0.1,
+):
+    # width
+    figsize = (15, 3)
+    label_fontsize = 15
+
+    categories: list[str] = list(parameter_labels.values())
+    f, ax = plt.subplots(figsize=figsize)
+
+    ax.bar(categories, ST, label='ST',
+           color="tab:orange",
+           alpha=1.0,
+           edgecolor="black",
+           yerr=ST_conf, capsize=5
+           )
+
+    ax.bar(categories, S1, label='S1', color="tab:blue",
+           edgecolor="black", yerr=S1_conf, capsize=5)
+
+
+    ax.set_xlabel('Parameter', fontsize=label_fontsize, fontweight="bold")
+    ax.set_ylabel('Sobol Index', fontsize=label_fontsize, fontweight="bold")
+    ax.set_ylim(bottom=ymin, top=ymax)
+    ax.grid(True, axis="y")
+    ax.tick_params(axis='x', labelrotation=90)
+    # ax.tick_params(axis='x', labelweight='bold')
+    ax.legend()
+
+    if title:
+        plt.suptitle(title, fontsize=20, fontweight="bold")
+
+    if fig_path:
+        plt.savefig(fig_path, dpi=300, bbox_inches="tight")
+    plt.show()
+