work on sensitivity analysis

Author: matthiaskoenig

pyproject.toml

@@ -48,8 +48,7 @@ dependencies = [
     "matplotlib",
     "pydantic",
     # dependencies
-    "diskcache>=5.6.3",
-    # "dill>=0.4.0",
+    "dill>=0.4.0",
     "SAlib>=1.5.2",
     "petab>=0.7.0",
     # "tables>=3.10.2",

src/sbmlsim/sensitivity/analysis.py

@@ -825,6 +825,3 @@ def run_sensitivity_analysis(
             fig_path=sa.results_path / f"sampling_sensitivity_N{sa.N}.png",
         )
 
-
-
-                )

src/sbmlsim/sensitivity/plots.py

@@ -117,45 +117,4 @@ def calculate_subset(df, cutoff=0.01) -> pd.DataFrame:
     plt.show()
 
 
-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()
-
 

src/sbmlsim/sensitivity/sobol.py

@@ -7,6 +7,7 @@
 import numpy as np
 import xarray as xr
 
+
 import SALib
 from SALib import ProblemSpec
 from SALib.sample import saltelli
@@ -160,3 +161,46 @@ def plot_sobol_indices(
                     parameter_labels=parameter_labels,
                     ymax=np.max([1.05, ymax]),
                     ymin=np.min([-0.05, ymin]),
+                )
+
+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()
+