:orphan:

Plot Gallery
============

Pyopenms-viz plotting occurs by calling the `.plot()` method on a pandas dataframe. Mandatory Types include has several built in plots which can be set using the "kind" attribute



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. thumbnail-parent-div-close

.. raw:: html

    </div>

BOKEH Plots
===========

These examples are generated if `backend='ms_bokheh'`. Interactive plots are supported and rendering is typically faster than the PLOTLY backend. 



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time. This peakmap is quite clean because signals are extracted across the m/z dimension.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_peakmap_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_peakmap_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example plots a peakmap with marginals by setting add_marginals=True A chromatogram is shown along the x-axis and a spectrum is shown along the y-axis.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_peakmap_marginals_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_peakmap_marginals_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a chromatogram colored by mass trace. Since all fragment ion spectra coelute this provides strong evidence that the peptide is present.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_chromatogram_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_chromatogram_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Chromatogram ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example makes a simple plot This example shows how to use different approaches.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_mobilogram_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_mobilogram_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mobilogram ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum from extracted data. No binning is applied.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_spectrum_dia_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_spectrum_dia_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum of Extracted DIA Data ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum.  We can add the ion_annotation and sequence annotation by specifying these columns.">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_spectrum_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_spectrum_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum ms_bokeh</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we show how we can plot multiple chromatograms across runs together">

.. only:: html

  .. image:: /gallery/ms_bokeh/images/thumb/sphx_glr_plot_spyogenes_subplots_ms_bokeh_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_bokeh_plot_spyogenes_subplots_ms_bokeh.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot Spyogenes subplots ms_bokeh</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

MATPLOTLIB Plots
================

These plots can be generated by setting the `backend='ms_matplotlib'`. Matplotlib is useful for generating static publication quality plots.



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time. This peakmap is quite clean because signals are extracted across the m/z dimension.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_peakmap_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_peakmap_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time, plotted in 3D.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_peakmap_3D_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_peakmap_3D_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Extracted PeakMap 3D ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example plots a peakmap with marginals by setting add_marginals=True A chromatogram is shown along the x-axis and a spectrum is shown along the y-axis.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_peakmap_marginals_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_peakmap_marginals_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a chromatogram colored by mass trace. Since all fragment ion spectra coelute this provides strong evidence that the peptide is present.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_chromatogram_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_chromatogram_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Chromatogram ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example makes a simple plot This example shows how to use different approaches.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_mobilogram_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_mobilogram_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mobilogram ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum.  We can add the ion_annotation and sequence annotation by specifying these columns.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_spectrum_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_spectrum_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum from extracted data. No binning is applied.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_spectrum_dia_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_spectrum_dia_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum of Extracted DIA Data ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time, plotted in 3D.">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_peakmap_3D_highlight_peptide_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_peakmap_3D_highlight_peptide_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Color Targeted Peptide PeakMap 3D ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how different binning levels affect peak map visualization">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_peakmap_binning_demonstration_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_peakmap_binning_demonstration_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot Peakmap Binning Demonstration</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we use a dummy spectrum example to investigate spectrum binning. ">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_investigate_spectrum_binning_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_investigate_spectrum_binning_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Investigate Spctrum Binning ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we show how we can plot multiple chromatograms across runs together">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_spyogenes_subplots_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_spyogenes_subplots_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot Spyogenes subplots ms_matplotlib</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows the code required to plot the d-fructose example in the manuscript.  The mzML file is from the the Human Metabolome Database (ID: HMDB0000660)">

.. only:: html

  .. image:: /gallery/ms_matplotlib/images/thumb/sphx_glr_plot_manuscript_d_fructose_spectrum_prediction_ms_matplotlib_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_matplotlib_plot_manuscript_d_fructose_spectrum_prediction_ms_matplotlib.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Manuscript d Fructose Example ms_matplotlib</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

PLOTLY Plots
============

These plots can be generated by setting the `backend='ms_plotly'`. PLOTLY plots inferfances well with StreamLit WebApps and allow for interactive 3D plots. Rendering is typically slower than the BOKEH backend.



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time. This peakmap is quite clean because signals are extracted across the m/z dimension.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_peakmap_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_peakmap_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time, plotted in 3D.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_peakmap_3D_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_peakmap_3D_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Extracted PeakMap 3D ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example plots a peakmap with marginals by setting add_marginals=True A chromatogram is shown along the x-axis and a spectrum is shown along the y-axis.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_peakmap_marginals_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_peakmap_marginals_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">PeakMap ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a chromatogram colored by mass trace. Since all fragment ion spectra coelute this provides strong evidence that the peptide is present.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_chromatogram_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_chromatogram_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Chromatogram ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example makes a simple plot This example shows how to use different approaches.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_mobilogram_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_mobilogram_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mobilogram ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum from extracted data. No binning is applied.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_spectrum_dia_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_spectrum_dia_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum of Extracted DIA Data ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a spectrum.  We can add the ion_annotation and sequence annotation by specifying these columns.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_spectrum_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_spectrum_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Spectrum ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This shows a peakmap across m/z and retention time, plotted in 3D.">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_peakmap_3D_highlight_peptide_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_peakmap_3D_highlight_peptide_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Color Targeted Peptide PeakMap 3D ms_plotly</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Here we show how we can plot multiple chromatograms across runs together. In this rendering the plot is slightly cut off">

.. only:: html

  .. image:: /gallery/ms_plotly/images/thumb/sphx_glr_plot_spyogenes_subplots_ms_plotly_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_ms_plotly_plot_spyogenes_subplots_ms_plotly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot Spyogenes subplots ms_plotly</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:
   :includehidden:


   /gallery/ms_bokeh/index.rst
   /gallery/ms_matplotlib/index.rst
   /gallery/ms_plotly/index.rst


.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-gallery

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

      :download:`Download all examples in Python source code: gallery_python.zip </gallery/gallery_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: gallery_jupyter.zip </gallery/gallery_jupyter.zip>`


.. only:: html

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

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