.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gallery/ms_plotly/plot_peakmap_3D_highlight_peptide_ms_plotly.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` 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_plotly_plot_peakmap_3D_highlight_peptide_ms_plotly.py: Color Targeted Peptide PeakMap 3D ms_plotly ========================================== This shows a peakmap across m/z and retention time, plotted in 3D. .. GENERATED FROM PYTHON SOURCE LINES 7-27 .. raw:: html

.. code-block:: Python import pandas as pd from io import StringIO import requests import numpy as np pd.options.plotting.backend = "ms_plotly" # 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 0.303 seconds) .. _sphx_glr_download_gallery_ms_plotly_plot_peakmap_3D_highlight_peptide_ms_plotly.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_plotly/plot_peakmap_3D_highlight_peptide_ms_plotly.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_plotly.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_peakmap_3D_highlight_peptide_ms_plotly.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_peakmap_3D_highlight_peptide_ms_plotly.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_