.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/ms_matplotlib/plot_peakmap_3D_highlight_peptide_ms_matplotlib.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_matplotlib_plot_peakmap_3D_highlight_peptide_ms_matplotlib.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_matplotlib_plot_peakmap_3D_highlight_peptide_ms_matplotlib.py:


Color Targeted Peptide PeakMap 3D ms_matplotlib
==========================================

This shows a peakmap across m/z and retention time, plotted in 3D.

.. GENERATED FROM PYTHON SOURCE LINES 7-27



.. image-sg:: /gallery/ms_matplotlib/images/sphx_glr_plot_peakmap_3D_highlight_peptide_ms_matplotlib_001.png
   :alt: PeakMap
   :srcset: /gallery/ms_matplotlib/images/sphx_glr_plot_peakmap_3D_highlight_peptide_ms_matplotlib_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    /home/runner/work/pyopenms_viz/pyopenms_viz/pyopenms_viz/_matplotlib/core.py:247: UserWarning:

    The figure layout has changed to tight


    <Axes3D: title={'center': 'PeakMap'}, xlabel='Retention Time', ylabel='mass-to-charge', zlabel='Intensity'>





|

.. code-block:: Python

    import pandas as pd
    from io import StringIO
    import requests
    import numpy as np

    pd.options.plotting.backend = "ms_matplotlib"

    # download the file for example plotting
    url = "https://github.com/OpenMS/pyopenms_viz/releases/download/v0.1.5/TestMSExperimentDf.tsv"
    response = requests.get(url)
    response.raise_for_status()  # Check for any HTTP errors
    df = pd.read_csv(StringIO(response.text), sep="\t")

    # create column which labels the peaks belonging to the target peptide
    df['label'] = 'unknown'
    df.iloc[ (np.ceil(df.mz) < 272)  & (np.ceil(df.mz) > 266) & \
    (np.ceil(df.RT) < 237)  & (np.ceil(df.RT) > 212), 3] = "peptide"

    # plot
    df.plot(x="RT", y="mz", z="inty", zlabel="Intensity", by='label', kind="peakmap", plot_3d=True, height=800, width=900)


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

   **Total running time of the script:** (0 minutes 2.609 seconds)


.. _sphx_glr_download_gallery_ms_matplotlib_plot_peakmap_3D_highlight_peptide_ms_matplotlib.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_matplotlib/plot_peakmap_3D_highlight_peptide_ms_matplotlib.ipynb
        :alt: Launch binder
        :width: 150 px

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

      :download:`Download Jupyter notebook: plot_peakmap_3D_highlight_peptide_ms_matplotlib.ipynb <plot_peakmap_3D_highlight_peptide_ms_matplotlib.ipynb>`

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

      :download:`Download Python source code: plot_peakmap_3D_highlight_peptide_ms_matplotlib.py <plot_peakmap_3D_highlight_peptide_ms_matplotlib.py>`

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

      :download:`Download zipped: plot_peakmap_3D_highlight_peptide_ms_matplotlib.zip <plot_peakmap_3D_highlight_peptide_ms_matplotlib.zip>`


.. only:: html

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

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