.. _sphx_glr_gallery_ms_plotly:

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:

   /gallery/ms_plotly/plot_peakmap_ms_plotly
   /gallery/ms_plotly/plot_peakmap_3D_ms_plotly
   /gallery/ms_plotly/plot_peakmap_marginals_ms_plotly
   /gallery/ms_plotly/plot_chromatogram_ms_plotly
   /gallery/ms_plotly/plot_mobilogram_ms_plotly
   /gallery/ms_plotly/plot_spectrum_dia_ms_plotly
   /gallery/ms_plotly/plot_spectrum_ms_plotly
   /gallery/ms_plotly/plot_peakmap_3D_highlight_peptide_ms_plotly
   /gallery/ms_plotly/plot_spyogenes_subplots_ms_plotly