fix goodness_of_fit plot and add color parameter (#402)

* fix goodness_of_fit plot and add color parameter

---------

Co-authored-by: Daniel Weindl <daniel.weindl@uni-bonn.de>

Author: plakrisenko

petab/v1/measurements.py

@@ -289,7 +289,7 @@ def assert_overrides_match_parameter_count(
             )
         }
         if NOISE_FORMULA in observable_df.columns
-        else {obs_id: 0 for obs_id in observable_df.index.values}
+        else dict.fromkeys(observable_df.index.values, 0)
     )
 
     for _, row in measurement_df.iterrows():

petab/v1/visualize/plot_residuals.py

@@ -134,6 +134,7 @@ def plot_goodness_of_fit(
     petab_problem: Problem,
     simulations_df: str | Path | pd.DataFrame,
     size: tuple = (10, 7),
+    color=None,
     ax: plt.Axes | None = None,
 ) -> matplotlib.axes.Axes:
     """
@@ -148,6 +149,9 @@ def plot_goodness_of_fit(
         output data file.
     size:
         Figure size.
+    color:
+        The marker colors, matches the `c` parameter of
+        `matplotlib.pyplot.scatter`.
     ax:
         Axis object.
 
@@ -171,8 +175,8 @@ def plot_goodness_of_fit(
         parameter_dfs=petab_problem.parameter_df,
     )[0]
     slope, intercept, r_value, p_value, std_err = stats.linregress(
-        petab_problem.measurement_df["measurement"],
         simulations_df["simulation"],
+        petab_problem.measurement_df["measurement"],
     )  # x, y
 
     if ax is None:
@@ -182,6 +186,7 @@ def plot_goodness_of_fit(
     ax.scatter(
         petab_problem.measurement_df["measurement"],
         simulations_df["simulation"],
+        c=color,
     )
 
     ax.axis("square")

tests/v1/test_visualization.py

@@ -8,14 +8,14 @@
 
 import petab
 from petab.C import *
-from petab.visualize import (
+from petab.v1.visualize import (
     plot_goodness_of_fit,
     plot_residuals_vs_simulation,
     plot_with_vis_spec,
     plot_without_vis_spec,
 )
-from petab.visualize.lint import validate_visualization_df
-from petab.visualize.plotting import VisSpecParser
+from petab.v1.visualize.lint import validate_visualization_df
+from petab.v1.visualize.plotting import VisSpecParser
 
 # Avoid errors when plotting without X server
 plt.switch_backend("agg")