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fix goodness_of_fit plot and add color parameter #402

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Merged
plakrisenko merged 4 commits into from
Jul 8, 2025
Merged

fix goodness_of_fit plot and add color parameter #402

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38f5a81
fix goodness_of_fit plot and add color parameter
plakrisenko Jul 7, 2025
5de8558
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plakrisenko Jul 7, 2025
5604a78
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plakrisenko Jul 7, 2025
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dweindl Jul 8, 2025
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7 changes: 6 additions & 1 deletion petab/v1/visualize/plot_residuals.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
"""
Expand All @@ -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.

Expand All @@ -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:
Expand All @@ -182,6 +186,7 @@ def plot_goodness_of_fit(
ax.scatter(
petab_problem.measurement_df["measurement"],
simulations_df["simulation"],
c=color,
)

ax.axis("square")
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6 changes: 3 additions & 3 deletions tests/v1/test_visualization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
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