├── .binder ├── postBuild ├── requirements.txt └── runtime.txt ├── .github └── workflows │ ├── ci.yml │ ├── execute_notebooks.yml │ ├── python-publish.yml │ ├── release.yml │ ├── scripts │ ├── release.py │ ├── update_init_version.py │ └── version_update_script.py │ └── static.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── app.py ├── docs ├── API.rst ├── Data Formatting │ ├── Data Formatting.rst │ ├── alphatims.ipynb │ ├── pymzml.ipynb │ ├── pyopenms.ipynb │ ├── pyteomics.ipynb │ └── test.mzML ├── Getting Started.ipynb ├── Installation.rst ├── Parameters │ ├── Chromatogram.rst │ ├── Mobilogram.rst │ ├── Parameters.rst │ ├── PeakMap.rst │ ├── Spectrum.rst │ ├── basePlot.tsv │ ├── chromatogramPlot.tsv │ ├── mobilogramPlot.tsv │ ├── peakMapPlot.tsv │ └── spectrumPlot.tsv ├── _ext │ └── docstring_to_table.py ├── _static │ ├── OpenMS.svg │ ├── custom.css │ └── switcher.json ├── conf.py ├── docs_env.yml ├── gallery_scripts_template │ ├── GALLERY_HEADER.rst │ ├── GALLERY_HEADER_ms_bokeh.rst │ ├── GALLERY_HEADER_ms_matplotlib.rst │ ├── GALLERY_HEADER_ms_plotly.rst │ ├── plot_chromatogram.py │ ├── plot_investigate_spectrum_binning_ms_matplotlib.py │ ├── plot_manuscript_d_fructose_spectrum_prediction_ms_matplotlib.py │ ├── plot_mobilogram.py │ ├── plot_peakmap.py │ ├── plot_peakmap_3D.py │ ├── plot_peakmap_3D_highlight_peptide.py │ ├── plot_peakmap_binning_demonstration_ms_matplotlib.py │ ├── plot_peakmap_marginals.py │ ├── plot_spectrum.py │ ├── plot_spectrum_dia.py │ ├── plot_spyogenes_subplots_ms_bokeh.py │ ├── plot_spyogenes_subplots_ms_matplotlib.py │ └── plot_spyogenes_subplots_ms_plotly.py ├── img │ ├── figure1.svg │ └── pyOpenMSviz_logo_color.png ├── index.rst ├── readme.md ├── requirements.txt ├── sg_execution_times.rst └── templates │ └── class.rst ├── nbs ├── FullSpectrumPlotting.ipynb ├── Spectrum.ipynb ├── manuscript_d_fructose_spectrum_prediction.ipynb ├── manuscript_gallery.ipynb ├── manuscript_spyogenes_subplots.ipynb ├── manuscript_supp_config_gallery.ipynb ├── matplotlib_subplot_tutorial.ipynb └── pyopenms_viz_tutorial.ipynb ├── pyopenms_viz ├── .gitignore ├── __init__.py ├── _bokeh │ ├── __init__.py │ └── core.py ├── _config.py ├── _core.py ├── _matplotlib │ ├── __init__.py │ └── core.py ├── _misc.py ├── _plotly │ ├── __init__.py │ └── core.py ├── assets │ └── img │ │ ├── feature_boundary.png │ │ └── peak_boundary.png ├── constants.py ├── test │ └── test_data │ │ └── README.md └── testing │ ├── BokehSnapshotExtension.py │ ├── MatplotlibSnapshotExtension.py │ ├── NumpySnapshotExtension.py │ ├── PandasSnapshotExtension.py │ ├── PlotlySnapshotExtension.py │ └── __init__.py ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt └── test ├── __snapshots__ ├── test_chromatogram │ ├── test_chromatogram_plot[ms_bokeh-kwargs0].html │ ├── test_chromatogram_plot[ms_bokeh-kwargs1].html │ ├── test_chromatogram_plot[ms_bokeh-kwargs2].html │ ├── test_chromatogram_plot[ms_bokeh-kwargs3].html │ ├── test_chromatogram_plot[ms_bokeh-kwargs4].html │ ├── test_chromatogram_plot[ms_matplotlib-kwargs0].png │ ├── test_chromatogram_plot[ms_matplotlib-kwargs1].png │ ├── test_chromatogram_plot[ms_matplotlib-kwargs2].png │ ├── test_chromatogram_plot[ms_matplotlib-kwargs3].png │ ├── test_chromatogram_plot[ms_matplotlib-kwargs4].png │ ├── test_chromatogram_plot[ms_plotly-kwargs0].json │ ├── test_chromatogram_plot[ms_plotly-kwargs1].json │ ├── test_chromatogram_plot[ms_plotly-kwargs2].json │ ├── test_chromatogram_plot[ms_plotly-kwargs3].json │ ├── test_chromatogram_plot[ms_plotly-kwargs4].json │ ├── test_chromatogram_with_annotation[ms_bokeh-kwargs0].html │ ├── test_chromatogram_with_annotation[ms_matplotlib-kwargs0].png │ └── test_chromatogram_with_annotation[ms_plotly-kwargs0].json ├── test_mobilogram │ ├── test_mobilogram_plot[ms_bokeh-kwargs0].html │ ├── test_mobilogram_plot[ms_bokeh-kwargs1].html │ ├── test_mobilogram_plot[ms_bokeh-kwargs2].html │ ├── test_mobilogram_plot[ms_bokeh-kwargs3].html │ ├── test_mobilogram_plot[ms_matplotlib-kwargs0].png │ ├── test_mobilogram_plot[ms_matplotlib-kwargs1].png │ ├── test_mobilogram_plot[ms_matplotlib-kwargs2].png │ ├── test_mobilogram_plot[ms_matplotlib-kwargs3].png │ ├── test_mobilogram_plot[ms_plotly-kwargs0].json │ ├── test_mobilogram_plot[ms_plotly-kwargs1].json │ ├── test_mobilogram_plot[ms_plotly-kwargs2].json │ └── test_mobilogram_plot[ms_plotly-kwargs3].json ├── test_peakmap │ ├── test_peakmap_mz_im[ms_bokeh].html │ ├── test_peakmap_mz_im[ms_matplotlib].png │ ├── test_peakmap_mz_im[ms_plotly].json │ ├── test_peakmap_plot[ms_bokeh-kwargs0].html │ ├── test_peakmap_plot[ms_bokeh-kwargs1].html │ ├── test_peakmap_plot[ms_bokeh-kwargs2].html │ ├── test_peakmap_plot[ms_bokeh-kwargs3].html │ ├── test_peakmap_plot[ms_bokeh-kwargs4].html │ ├── test_peakmap_plot[ms_matplotlib-kwargs0].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs1].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs2].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs3].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs4].png │ ├── test_peakmap_plot[ms_plotly-kwargs0].json │ ├── test_peakmap_plot[ms_plotly-kwargs1].json │ ├── test_peakmap_plot[ms_plotly-kwargs2].json │ ├── test_peakmap_plot[ms_plotly-kwargs3].json │ └── test_peakmap_plot[ms_plotly-kwargs4].json ├── test_peakmap3d │ ├── test_peakmap_plot[ms_matplotlib-kwargs0].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs1].png │ ├── test_peakmap_plot[ms_matplotlib-kwargs2].png │ ├── test_peakmap_plot[ms_plotly-kwargs0].json │ ├── test_peakmap_plot[ms_plotly-kwargs1].json │ └── test_peakmap_plot[ms_plotly-kwargs2].json ├── test_peakmap_marginals │ ├── test_peakmap_marginals[ms_bokeh].html │ ├── test_peakmap_marginals[ms_matplotlib].png │ ├── test_peakmap_marginals[ms_plotly].json │ ├── test_peakmap_mz_im[ms_bokeh].html │ ├── test_peakmap_mz_im[ms_matplotlib].png │ └── test_peakmap_mz_im[ms_plotly].json └── test_spectrum │ ├── test_mirror_spectrum[ms_bokeh].html │ ├── test_mirror_spectrum[ms_matplotlib].png │ ├── test_mirror_spectrum[ms_plotly].json │ ├── test_spectrum_binning[ms_bokeh-kwargs0].html │ ├── test_spectrum_binning[ms_bokeh-kwargs1].html │ ├── test_spectrum_binning[ms_bokeh-kwargs2].html │ ├── test_spectrum_binning[ms_bokeh-kwargs3].html │ ├── test_spectrum_binning[ms_bokeh-kwargs4].html │ ├── test_spectrum_binning[ms_matplotlib-kwargs0].png │ ├── test_spectrum_binning[ms_matplotlib-kwargs1].png │ ├── test_spectrum_binning[ms_matplotlib-kwargs2].png │ ├── test_spectrum_binning[ms_matplotlib-kwargs3].png │ ├── test_spectrum_binning[ms_matplotlib-kwargs4].png │ ├── test_spectrum_binning[ms_plotly-kwargs0].json │ ├── test_spectrum_binning[ms_plotly-kwargs1].json │ ├── test_spectrum_binning[ms_plotly-kwargs2].json │ ├── test_spectrum_binning[ms_plotly-kwargs3].json │ ├── test_spectrum_binning[ms_plotly-kwargs4].json │ ├── test_spectrum_plot[ms_bokeh-kwargs0].html │ ├── test_spectrum_plot[ms_bokeh-kwargs1].html │ ├── test_spectrum_plot[ms_bokeh-kwargs2].html │ ├── test_spectrum_plot[ms_bokeh-kwargs3].html │ ├── test_spectrum_plot[ms_matplotlib-kwargs0].png │ ├── test_spectrum_plot[ms_matplotlib-kwargs1].png │ ├── test_spectrum_plot[ms_matplotlib-kwargs2].png │ ├── test_spectrum_plot[ms_matplotlib-kwargs3].png │ ├── test_spectrum_plot[ms_plotly-kwargs0].json │ ├── test_spectrum_plot[ms_plotly-kwargs1].json │ ├── test_spectrum_plot[ms_plotly-kwargs2].json │ ├── test_spectrum_plot[ms_plotly-kwargs3].json │ ├── test_spectrum_plot_with_peak_color[ms_bokeh-kwargs0].html │ ├── test_spectrum_plot_with_peak_color[ms_bokeh-kwargs1].html │ ├── test_spectrum_plot_with_peak_color[ms_matplotlib-kwargs0].png │ ├── test_spectrum_plot_with_peak_color[ms_matplotlib-kwargs1].png │ ├── test_spectrum_plot_with_peak_color[ms_plotly-kwargs0].json │ ├── test_spectrum_plot_with_peak_color[ms_plotly-kwargs1].json │ ├── test_spectrum_with_annotations[ms_bokeh-kwargs0].html │ ├── 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