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Vis: Make line plot markers configurable #254

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merged 4 commits into from
Apr 16, 2024
Merged

Vis: Make line plot markers configurable #254

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ff97982
Vis: Make line plot markers configurable
dweindl Apr 16, 2024
6f3a78d
dict
dweindl Apr 16, 2024
a6efcc6
Merge branch 'develop' into vis_lineplot_style
dweindl Apr 16, 2024
3571743
Merge branch 'develop' into vis_lineplot_style
dweindl Apr 16, 2024
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54 changes: 28 additions & 26 deletions petab/visualize/plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,22 @@
__all__ = ["Plotter", "MPLPlotter", "SeabornPlotter"]


#: Line style (:class:`matplotlib.lines.Line2D` options) for the measurement
# data in line plots
measurement_line_kwargs = {
"linestyle": "-.",
"marker": "x",
"markersize": 10,
}
#: Line style (:class:`matplotlib.lines.Line2D` options) for the simulation
# data in line plots
simulation_line_kwargs = {
"linestyle": "-",
"marker": "o",
"markersize": 10,
}


class Plotter(ABC):
"""
Plotter abstract base class.
Expand Down Expand Up @@ -78,7 +94,7 @@ def generate_lineplot(
splitaxes_params: dict,
) -> Tuple[matplotlib.axes.Axes, matplotlib.axes.Axes]:
"""
Generate lineplot.
Generate line plot.

It is possible to plot only data or only simulation or both.

Expand Down Expand Up @@ -136,19 +152,15 @@ def generate_lineplot(
p = ax.plot(
cond,
replicates[:, 0],
linestyle="-.",
marker="x",
markersize=10,
label=label_base,
**measurement_line_kwargs,
)

# plot other replicates with the same color
ax.plot(
cond,
replicates[:, 1:],
linestyle="-.",
marker="x",
markersize=10,
**measurement_line_kwargs,
color=p[0].get_color(),
)

Expand Down Expand Up @@ -177,9 +189,8 @@ def generate_lineplot(
scond,
smean,
snoise,
linestyle="-.",
marker=".",
label=label_base,
**measurement_line_kwargs,
)

# simulations should have the same colors if both measurements
Expand Down Expand Up @@ -229,11 +240,10 @@ def generate_lineplot(
p = ax.plot(
xs,
ys,
linestyle="-",
marker="o",
markevery=every,
label=label_base + " simulation",
color=simu_color,
**simulation_line_kwargs,
)
# lines at t=inf should have the same colors also in case
# only simulations are plotted
Expand Down Expand Up @@ -628,23 +638,19 @@ def _line_plot_at_t_inf(
p = ax_inf.plot(
timepoints_inf,
[replicates[0]] * 3,
linestyle="-.",
marker="x",
markersize=10,
markevery=[1],
label=label_base + " simulation",
color=color,
**measurement_line_kwargs,
)

# plot other replicates with the same color
ax_inf.plot(
timepoints_inf,
[replicates[1:]] * 3,
linestyle="-.",
marker="x",
markersize=10,
markevery=[1],
color=p[0].get_color(),
**measurement_line_kwargs,
)
else:
p = ax_inf.plot(
Expand All @@ -653,17 +659,16 @@ def _line_plot_at_t_inf(
measurements_data_to_plot_inf["mean"],
measurements_data_to_plot_inf["mean"],
],
linestyle="-.",
color=color,
**measurement_line_kwargs,
)
ax_inf.errorbar(
t_inf,
measurements_data_to_plot_inf["mean"],
measurements_data_to_plot_inf[noise_col],
linestyle="-.",
marker=".",
label=label_base + " simulation",
color=p[0].get_color(),
**measurement_line_kwargs,
)

if color is None:
Expand All @@ -687,30 +692,27 @@ def _line_plot_at_t_inf(
p = ax_inf.plot(
timepoints_inf,
[replicates[0]] * 3,
linestyle="-",
marker="o",
markevery=[1],
label=label_base,
color=color,
**simulation_line_kwargs,
)

# plot other replicates with the same color
ax_inf.plot(
timepoints_inf,
[replicates[1:]] * 3,
linestyle="-",
marker="o",
markevery=[1],
color=p[0].get_color(),
**simulation_line_kwargs,
)
else:
ax_inf.plot(
timepoints_inf,
[simulations_data_to_plot_inf["mean"]] * 3,
linestyle="-",
marker="o",
markevery=[1],
color=color,
**simulation_line_kwargs,
)

ax.set_xlim(right=ax_finite_right_limit)
Expand Down
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