.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "_examples\visualization\plot_graphics_antibiogram.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download__examples_visualization_plot_graphics_antibiogram.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr__examples_visualization_plot_graphics_antibiogram.py:


Graphics Antibiogram example
============================

.. GENERATED FROM PYTHON SOURCE LINES 5-87



.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /_examples/visualization/images/sphx_glr_plot_graphics_antibiogram_001.png
         :alt: Antibiogram (euclidean, weighted)
         :srcset: /_examples/visualization/images/sphx_glr_plot_graphics_antibiogram_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /_examples/visualization/images/sphx_glr_plot_graphics_antibiogram_002.png
         :alt: Antibiogram (euclidean, weighted)
         :srcset: /_examples/visualization/images/sphx_glr_plot_graphics_antibiogram_002.png
         :class: sphx-glr-multi-img





.. code-block:: default
   :lineno-start: 6


    # Libraries
    from __future__ import division

    # Libraries
    import sys
    import numpy as np
    import pandas as pd
    import seaborn as sns
    import matplotlib as mpl
    import matplotlib.pyplot as plt

    #
    from pyamr.graphics.antibiogram import Antibiogram


    # Configure seaborn style (context=talk)
    sns.set(style="white")

    # Set matplotlib
    mpl.rcParams['xtick.labelsize'] = 9
    mpl.rcParams['ytick.labelsize'] = 9
    mpl.rcParams['axes.titlesize'] = 11
    mpl.rcParams['legend.fontsize'] = 9

    # Pandas configuration
    pd.set_option('display.max_colwidth', 40)
    pd.set_option('display.width', 300)
    pd.set_option('display.precision', 4)

    # Numpy configuration
    np.set_printoptions(precision=2)

    # -------------------------------------------------------------------------
    #                            helper methods
    # -------------------------------------------------------------------------


    # -------------------------------------------------------------------------
    #                                main
    # -------------------------------------------------------------------------
    # Data path.
    path = '../../pyamr/fixtures/fixture_antibiogram.csv'

    # -------------------------------
    # Load data
    # -------------------------------
    # Load
    dataframe = pd.read_csv(path)

    # -------------------------------
    # Create object
    # -------------------------------
    # Antibiogram plotter
    antibiogram = Antibiogram(column_organism='organismCode',
                              column_antibiotic='antibioticCode',
                              column_genus='specieName',
                              column_category='antibioticClass',
                              column_index='sari')

    # Fit antibiogram
    antibiogram = antibiogram.fit(dataframe)

    # ---------
    # Example 1
    # ----------
    antibiogram.plot(organisms=['ECOL', 'SAUR'], figsize=(15, 3))

    # ---------
    # Example 2
    # ---------
    antibiogram.plot(genera=['staphylococcus',
                             'klebsiella',
                             'streptococcus',
                             'enterococcus',
                             'enterobacter'],
                     categories=None,
                     method='weighted',
                     metric='euclidean',
                     figsize=(16, 9))

    # Show
    plt.show()

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

   **Total running time of the script:** ( 0 minutes  2.109 seconds)


.. _sphx_glr_download__examples_visualization_plot_graphics_antibiogram.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example




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

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

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

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


.. only:: html

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

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