PyOpenMS-Viz
============

Welcome to PyOpenMS-Viz Documentation! PyOpenMS-Viz is a visualization package for mass spectrometry data directly from pandas dataframes.

Key Features Include:

* **DataFrame Based Plotting** - Plot directly from a pandas dataframe object
* **Interactive and Static Plotting** - Multiple backends supported including matplotlib, bokeh, and plotly
* **Usage Flexibility** - User-friendly web-based dashboard for quick visualizations, advanced python package for more complex applications 

Quick Start
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Installation
------------

.. code-block:: shell

    pip install pyopenms-viz 

Plotting a Spectrum
-------------------

.. code-block:: python

    import pandas as pd
    ms_data = pd.read_csv("path/to/ms_data.csv")
    pd.set_option("plotting.backend", "ms_bokeh")  # try changing backend to "ms_plotly" or "ms_matplotlib"
    ms_data.plot(x="m/z", y="intensity", kind="spectrum") 
    
Plotting a Chromatogram
-----------------------

.. code-block:: python

    import pandas as pd
    ms_data = pd.read_csv("path/to/ms_data.csv")
    pd.set_option("plotting.backend", "ms_bokeh")  # try changing backend to "ms_plotly" or "ms_matplotlib"
    ms_data.plot(x="rt", y="intensity", kind="chromatogram")

Support
*******

If you are having issues or would like to propose a new feature, please use the `issues tracker <https://github.com/jcharkow/pyopenms-viz/issues>`_.

License
*******

This project is licensed under the BSD 3-Clause license.

Citation
********
If PyOpenMS-Viz was useful in your research, please cite the following:

User Guide
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.. toctree::
   :maxdepth: 1
   :glob:

   Installation
   Getting Started
   Parameters/Parameters
   gallery/index
   Data Formatting/Data Formatting
   API