Skip to content

fix goodness_of_fit plot and add color parameter #402

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

fix goodness_of_fit plot and add color parameter #402

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
38f5a81
fix goodness_of_fit plot and add color parameter
plakrisenko Jul 7, 2025
5de8558
style
plakrisenko Jul 7, 2025
5604a78
style
plakrisenko Jul 7, 2025
f48902e
ruff
dweindl Jul 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion petab/v1/measurements.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down
7 changes: 6 additions & 1 deletion petab/v1/visualize/plot_residuals.py
View file
Open in desktop
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")
Expand Down
6 changes: 3 additions & 3 deletions tests/v1/test_visualization.py
View file
Open in desktop
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")
Expand Down