Merge branch 'develop' into abstract_model

PEtab-dev · May 12, 2022 · 003ab5d · 003ab5d
2 parents 83a2989 + 44ff4af
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diff --git a/doc/conf.py b/doc/conf.py
@@ -64,9 +64,6 @@
     'build/html',
     '**.ipynb_checkpoints',
     'logo/LICENSE.md',
-    # TODO update and un-exclude
-    'example/example_visualization.ipynb',
-    'example/example_visualization_without_visspec.ipynb',
 ]
 
 master_doc = 'index'

diff --git a/doc/example.rst b/doc/example.rst
@@ -9,6 +9,8 @@ The following examples should help to get a better idea of how to use the PEtab
    :maxdepth: 1
 
    example/example_petablint.ipynb
+   example/example_visualization.ipynb
+   example/example_visualization_without_visspec.ipynb
    example/example_visualization_with_visspec.ipynb
 
 Examples of systems biology parameter estimation problems specified in PEtab

diff --git a/doc/example/example_Isensee/Isensee_visualizationSpecification.tsv b/doc/example/example_Isensee/Isensee_visualizationSpecification.tsv
@@ -30,6 +30,6 @@ plot4	JI09_151102_Drg421_418_Age	LinePlot	MeanAndSD	JI09_151102_Drg421_418_Age__
 plot5	JI09_160126_Drg449_444_CycNuc	BarPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__ctrl	condition	0	Condition	pRII_Western	0	pRII_Western	Ctrl	lin	lin
 plot5	JI09_160126_Drg449_444_CycNuc	BarPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100	condition	0	Condition	pRII_Western	0	pRII_Western	IBMX(100)/Fsk(10)	lin	lin
 plot5	JI09_160126_Drg449_444_CycNuc	BarPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10	condition	0	Condition	pRII_Western	0	pRII_Western	Sp8-Br-cAMPS-AM(10)	lin	lin
-plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__ctrl	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Ctrl	lin	lin
-plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Fsk	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Fsk(10)	lin	lin
-plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Sp8-Br-cAMPS-AM(10)	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	LinePlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__ctrl	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Ctrl	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	LinePlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Fsk	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Fsk(10)	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	LinePlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Sp8-Br-cAMPS-AM(10)	lin	lin
diff --git a/doc/example/example_Isensee/Isensee_visualizationSpecification_scatterplot.tsv b/doc/example/example_Isensee/Isensee_visualizationSpecification_scatterplot.tsv
@@ -0,0 +1,7 @@
+plotId	plotName	plotTypeSimulation	plotTypeData	datasetId	xValues	xOffset	xLabel	yValues	yOffset	yLabel	legendEntry	xScale	yScale
+plot5	JI09_160126_Drg449_444_CycNuc	ScatterPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__ctrl	condition	0	Condition	pRII_Western	0	pRII_Western	Ctrl	lin	lin
+plot5	JI09_160126_Drg449_444_CycNuc	ScatterPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__Fsk10_and_IBMX100	condition	0	Condition	pRII_Western	0	pRII_Western	IBMX(100)/Fsk(10)	lin	lin
+plot5	JI09_160126_Drg449_444_CycNuc	ScatterPlot	MeanAndSD	JI09_160126_Drg449_444_CycNuc__Sp8_Br_cAMPS_AM10	condition	0	Condition	pRII_Western	0	pRII_Western	Sp8-Br-cAMPS-AM(10)	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__ctrl	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Ctrl	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Fsk	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Fsk(10)	lin	lin
+plot6	JI09_160201_Drg453-452_CycNuc	ScatterPlot	MeanAndSD	JI09_160201_Drg453-452_CycNuc__Sp8_Br_cAMPS_AM	time	0	Time [min]	Calpha_Microscopy	0	Calpha_Microscopy	Sp8-Br-cAMPS-AM(10)	lin	lin
diff --git a/doc/example/example_visualization.ipynb b/doc/example/example_visualization.ipynb
diff --git a/doc/example/example_visualization_without_visspec.ipynb b/doc/example/example_visualization_without_visspec.ipynb
diff --git a/petab/visualize/plotter.py b/petab/visualize/plotter.py
@@ -170,7 +170,6 @@ def generate_barplot(self, ax: 'matplotlib.pyplot.Axes',
         # TODO: plotTypeData == REPLICATE?
         noise_col = self._error_column_for_plot_type_data(plotTypeData)
 
-        simu_colors = None
         measurements_to_plot, simulations_to_plot = \
             self.data_provider.get_data_to_plot(dataplot,
                                                 plotTypeData == PROVIDED)
@@ -191,15 +190,14 @@ def generate_barplot(self, ax: 'matplotlib.pyplot.Axes',
         color = plt.rcParams["axes.prop_cycle"].by_key()["color"][0]
 
         if measurements_to_plot is not None:
-            p = ax.bar(x_name, measurements_to_plot.data_to_plot['mean'],
-                       yerr=measurements_to_plot.data_to_plot[noise_col],
-                       color=color, **bar_kwargs, label='measurement')
-            simu_colors = p[0].get_facecolor()
+            ax.bar(x_name, measurements_to_plot.data_to_plot['mean'],
+                   yerr=measurements_to_plot.data_to_plot[noise_col],
+                   color=color, **bar_kwargs, label='measurement')
 
         if simulations_to_plot is not None:
             bar_kwargs['width'] = -bar_kwargs['width']
             ax.bar(x_name, simulations_to_plot.data_to_plot['mean'],
-                   color='white', edgecolor=simu_colors, **bar_kwargs,
+                   color='white', edgecolor=color, **bar_kwargs,
                    label='simulation')
 
     def generate_scatterplot(self, ax: 'matplotlib.pyplot.Axes',
@@ -222,7 +220,7 @@ def generate_scatterplot(self, ax: 'matplotlib.pyplot.Axes',
             self.data_provider.get_data_to_plot(dataplot,
                                                 plotTypeData == PROVIDED)
 
-        if simulations_to_plot is None:
+        if simulations_to_plot is None or measurements_to_plot is None:
             raise NotImplementedError('Scatter plots do not work without'
                                       ' simulation data')
         ax.scatter(measurements_to_plot.data_to_plot['mean'],

diff --git a/tests/test_visualization.py b/tests/test_visualization.py
@@ -102,6 +102,12 @@ def vis_spec_file_Isensee_replicates():
            / "Isensee_visualizationSpecification_replicates.tsv"
 
 
+@pytest.fixture
+def vis_spec_file_Isensee_scatterplot():
+    return EXAMPLE_DIR / "example_Isensee" \
+           / "Isensee_visualizationSpecification_scatterplot.tsv"
+
+
 @pytest.fixture
 def simulation_file_Isensee():
     return EXAMPLE_DIR / "example_Isensee" / "Isensee_simulationData.tsv"
@@ -124,6 +130,15 @@ def test_visualization_replicates(data_file_Isensee,
                        data_file_Isensee, simulation_file_Isensee)
 
 
+def test_visualization_scatterplot(data_file_Isensee,
+                                   condition_file_Isensee,
+                                   vis_spec_file_Isensee_scatterplot,
+                                   simulation_file_Isensee):
+    plot_with_vis_spec(vis_spec_file_Isensee_scatterplot,
+                       condition_file_Isensee,
+                       data_file_Isensee, simulation_file_Isensee)
+
+
 def test_visualization_small_visu_file_w_datasetid(data_file_Fujita,
                                                    condition_file_Fujita,
                                                    visu_file_Fujita_small):