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Doc: Clean up visualization examples (#236)
The visualization examples were pretty redundant. Merged them into a single notebook. Removed redundant blocks. Furthermore: * Don't use deprecated `Problem.from_files` * Simplify by not loading all files separately * Fix grammar / typos * Add replicate plot example * Make plots more readable * ... :eyes: https://petab--236.org.readthedocs.build/projects/libpetab-python/en/236/example/example_visualization.html# Co-authored-by: Maren Philipps <[email protected]>
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‎doc/conf.py‎

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# myst_nb options
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# https://myst-nb.readthedocs.io/en/latest/configuration.html
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nb_execution_mode = "force"
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nb_execution_raise_on_error = True
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nb_execution_show_tb = True
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source_suffix = {
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".rst": "restructuredtext",

‎doc/example.rst‎

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example/example_petablint.ipynb
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example/example_visualization.ipynb
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example/example_visualization_without_visspec.ipynb
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example/example_visualization_with_visspec.ipynb
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Examples of systems biology parameter estimation problems specified in PEtab
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can be found in the `systems biology benchmark model collection <https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab>`_.

‎doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_datasetIds.tsv‎

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plotId plotTypeSimulation plotTypeData datasetId xValues legendEntry
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plot1 LinePlot provided model1_data1_pEGFR_tot time Data 1, pEGFR total
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plot1 LinePlot provided model1_data2_pEGFR_tot time Data 2, pEGFR total
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plot1 LinePlot provided model1_data3_pEGFR_tot time Data 3, pEGFR total
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plot1 LinePlot provided model1_data4_pEGFR_tot time Data 4, pEGFR total
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plot1 LinePlot provided model1_data5_pEGFR_tot time Data 5, pEGFR total
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plot1 LinePlot provided model1_data6_pEGFR_tot time Data 6, pEGFR total
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plot2 LinePlot provided model1_data1_pAkt_tot time Data 1, pAkt total
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plot2 LinePlot provided model1_data2_pAkt_tot time Data 2, pAkt total
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plot2 LinePlot provided model1_data3_pAkt_tot time Data 3, pAkt total
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plot2 LinePlot provided model1_data4_pAkt_tot time Data 4, pAkt total
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plot2 LinePlot provided model1_data5_pAkt_tot time Data 5, pAkt total
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plot2 LinePlot provided model1_data6_pAkt_tot time Data 6, pAkt total
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plot3 LinePlot provided model1_data1_pS6_tot time Data 1, pS6 total
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plot3 LinePlot provided model1_data2_pS6_tot time Data 2, pS6 total
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plot3 LinePlot provided model1_data3_pS6_tot time Data 3, pS6 total
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plot3 LinePlot provided model1_data4_pS6_tot time Data 4, pS6 total
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plot3 LinePlot provided model1_data5_pS6_tot time Data 5, pS6 total
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plot3 LinePlot provided model1_data6_pS6_tot time Data 6, pS6 total
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plotId plotTypeData datasetId xValues legendEntry
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plot1 provided model1_data1_pEGFR_tot time Data 1, pEGFR total
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plot1 provided model1_data2_pEGFR_tot time Data 2, pEGFR total
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plot1 provided model1_data3_pEGFR_tot time Data 3, pEGFR total
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plot1 provided model1_data4_pEGFR_tot time Data 4, pEGFR total
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plot1 provided model1_data5_pEGFR_tot time Data 5, pEGFR total
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plot1 provided model1_data6_pEGFR_tot time Data 6, pEGFR total
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plot2 provided model1_data1_pAkt_tot time Data 1, pAkt total
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plot2 provided model1_data2_pAkt_tot time Data 2, pAkt total
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plot2 provided model1_data3_pAkt_tot time Data 3, pAkt total
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plot2 provided model1_data4_pAkt_tot time Data 4, pAkt total
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plot2 provided model1_data5_pAkt_tot time Data 5, pAkt total
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plot2 provided model1_data6_pAkt_tot time Data 6, pAkt total
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plot3 provided model1_data1_pS6_tot time Data 1, pS6 total
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plot3 provided model1_data2_pS6_tot time Data 2, pS6 total
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plot3 provided model1_data3_pS6_tot time Data 3, pS6 total
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plot3 provided model1_data4_pS6_tot time Data 4, pS6 total
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plot3 provided model1_data5_pS6_tot time Data 5, pS6 total
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plot3 provided model1_data6_pS6_tot time Data 6, pS6 total

‎doc/example/example_Fujita/visuSpecs/Fujita_visuSpec_individual_datasets.tsv‎

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plotId plotTypeSimulation plotTypeData datasetId xValues
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plot1 LinePlot provided model1_data1_pEGFR_tot time
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plot2 LinePlot provided model1_data2_pEGFR_tot time
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plot2 LinePlot provided model1_data3_pEGFR_tot time
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plot3 LinePlot provided model1_data4_pEGFR_tot time
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plot3 LinePlot provided model1_data5_pEGFR_tot time
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plot3 LinePlot provided model1_data6_pEGFR_tot time
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plotId plotTypeData datasetId xValues
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plot1 provided model1_data1_pEGFR_tot time
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plot2 provided model1_data2_pEGFR_tot time
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plot2 provided model1_data3_pEGFR_tot time
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plot3 provided model1_data4_pEGFR_tot time
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plot3 provided model1_data5_pEGFR_tot time
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plot3 provided model1_data6_pEGFR_tot time

‎doc/example/example_Isensee/Isensee.yaml‎

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format_version: 1
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parameter_file:
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problems:
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- condition_files:
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- Isensee_experimentalCondition.tsv
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measurement_files:
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- Isensee_measurementData.tsv
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observable_files: []
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sbml_files: []
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visualization_files:
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- Isensee_visualizationSpecification.tsv

‎doc/example/example_Isensee/Isensee_no_vis.yaml‎

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format_version: 1
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parameter_file:
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problems:
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- condition_files:
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- Isensee_experimentalCondition.tsv
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measurement_files:
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- Isensee_measurementData.tsv
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observable_files: []
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sbml_files: []

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