.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/ms_bokeh/plot_spectrum_ms_bokeh.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_gallery_ms_bokeh_plot_spectrum_ms_bokeh.py>`
        to download the full example code or to run this example in your browser via Binder.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gallery_ms_bokeh_plot_spectrum_ms_bokeh.py:


Spectrum ms_bokeh
=======================================

This example shows a spectrum.
We can add the ion_annotation and sequence annotation by specifying these columns.

.. GENERATED FROM PYTHON SOURCE LINES 8-27


.. bokeh-plot::
    :source-position: none
    
    from bokeh.plotting import show
    
    import pandas as pd
    from pyopenms_viz.util import download_file
    
    pd.options.plotting.backend = "ms_bokeh"
    
    url = "https://zenodo.org/records/17904352/files/TestSpectrumDf.tsv?download=1"
    local_path = "TestSpectrumDf.tsv"
    download_file(url, local_path)
    df = pd.read_csv(local_path, sep="\t")
    
    # mirror a reference spectrum with ion and sequence annoations
    df.plot(
        x="mz",
        y="intensity",
        kind="spectrum",
        ion_annotation="ion_annotation",
        sequence_annotation="sequence",
    )
    

.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Annotation color: None


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    <br />
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|

.. code-block:: Python


    import pandas as pd
    from pyopenms_viz.util import download_file

    pd.options.plotting.backend = "ms_bokeh"

    url = "https://zenodo.org/records/17904352/files/TestSpectrumDf.tsv?download=1"
    local_path = "TestSpectrumDf.tsv"
    download_file(url, local_path)
    df = pd.read_csv(local_path, sep="\t")

    # mirror a reference spectrum with ion and sequence annoations
    df.plot(
        x="mz",
        y="intensity",
        kind="spectrum",
        ion_annotation="ion_annotation",
        sequence_annotation="sequence",
    )


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 1.728 seconds)


.. _sphx_glr_download_gallery_ms_bokeh_plot_spectrum_ms_bokeh.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://notebooks.gesis.org/binder/v2/gh/OpenMS/pyopenms_viz/gh_pages?filepath=notebooks/gallery/ms_bokeh/plot_spectrum_ms_bokeh.ipynb
        :alt: Launch binder
        :width: 150 px

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_spectrum_ms_bokeh.ipynb <plot_spectrum_ms_bokeh.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_spectrum_ms_bokeh.py <plot_spectrum_ms_bokeh.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_spectrum_ms_bokeh.zip <plot_spectrum_ms_bokeh.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_