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Merged
dweindl merged 8 commits into from
May 10, 2022
Merged

Update example notebooks #146

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4f1d3d1
remove plot_data_and_simulation
plakrisenko May 9, 2022
28750fa
move scatterplots to a separate visualization specification file
plakrisenko May 9, 2022
681021e
add scatterplot test
plakrisenko May 9, 2022
01661e6
scatterplot can be plotted only if both measurements and simulations …
plakrisenko May 9, 2022
ebdc5ee
fix plotting barplots with only simulation data
plakrisenko May 9, 2022
9241e45
code style
plakrisenko May 9, 2022
1384d05
un-exclude in doc/conf.py and add to examples.rst
plakrisenko May 9, 2022
5aaee29
remove jupyter notebook outputs
plakrisenko May 9, 2022
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1 change: 0 additions & 1 deletion doc/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,6 @@
'**.ipynb_checkpoints',
'logo/LICENSE.md',
# TODO update and un-exclude
'example/example_visualization.ipynb',
'example/example_visualization_without_visspec.ipynb',
]

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1 change: 1 addition & 0 deletions doc/example.rst
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Expand Up @@ -9,6 +9,7 @@ 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_with_visspec.ipynb

Examples of systems biology parameter estimation problems specified in PEtab
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6 changes: 3 additions & 3 deletions doc/example/example_Isensee/Isensee_visualizationSpecification.tsv
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Expand Up @@ -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
7 changes: 7 additions & 0 deletions doc/example/example_Isensee/Isensee_visualizationSpecification_scatterplot.tsv
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@@ -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
354 changes: 133 additions & 221 deletions doc/example/example_visualization.ipynb
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12 changes: 5 additions & 7 deletions petab/visualize/plotter.py
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Expand Up @@ -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)
Expand All @@ -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',
Expand All @@ -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'],
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15 changes: 15 additions & 0 deletions tests/test_visualization.py
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Expand Up @@ -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"
Expand All @@ -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):
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