.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "_examples/plotly/main06_treemap_v3.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        Click :ref:`here <sphx_glr_download__examples_plotly_main06_treemap_v3.py>`
        to download the full example code

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

.. _sphx_glr__examples_plotly_main06_treemap_v3.py:


06. Plot Treemap with NHS
-------------------------------

This example displays a Treemap using a portion of the NHS dataset. This
example needs ``pyAMR`` to load the corresponding data.

.. warning:: It is not completed!
.. warning:: It might take some time to load.
.. note:: It uses ``plotly.express`` rather than ``go.Treemap``.
.. note:: https://plotly.com/python/treemaps/

.. GENERATED FROM PYTHON SOURCE LINES 14-221




.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none


    '\n# Set custom data (not needed and inconsistent)\n#fig.data[0].customdata = dataframe.to_numpy()\n#fig.data[0].hovertemplate = htmp\n\n# Uncomment to check the customdata[i] information\n#fig.data[0].hovertemplate = #    guide_template(dataframe.columns.tolist())\n\n# Update: I\n#fig.update_traces(hovertemplate=\'labels=%{label}\')\n#fig.update_traces(texttemplate=\'Freq=%{value:.2f}<br>\')\nfig.update_traces(hovertemplate=htmp_guide)\n#fig.update_traces(hovertemplate=htmp)\n\n# Update: II\n# But it seems to me you want something like\n#fig.data[0].hovertemplate = \'%{label}<br>%{value}\'\n#fig.data[0].hovertemplate = \'%{Freq}<br>%{Antimicrobial Name}\'\n\nfig.update_layout(\n    margin={\n        \'l\': 0,\n        \'r\': 0,\n        \'b\': 0,\n        \'t\': 0,\n        \'pad\': 4\n     })\n# ----------------------------\n# Save\n# ----------------------------\n# Libraries\nimport time\nfrom pathlib import Path\n\n# Define pipeline path\npath = Path(\'./objects\') / \'plot_main08_treemap\'\nfilename = \'%s.html\' % time.strftime("%Y%m%d-%H%M%S")\n\n# Create folder (if it does not exist)\npath.mkdir(parents=True, exist_ok=True)\n\n# Save\nfig.write_html("%s/%s" % (path, filename))\n\n# Show\nshow(fig)\n'





|

.. code-block:: default
   :lineno-start: 14

    # Plotly

    import numpy as np
    import pandas as pd
    import plotly.express as px

    from plotly.io import show

    # Import own libraries
    from pyamr.core.sari import sari
    from pyamr.datasets.load import load_data_nhs

    try:
        __file__
        TERMINAL = True
    except:
        TERMINAL = False


    # Methods
    def build_hierarchical_dataframe(df, levels, value_column, color_columns=None):
        """
        Build a hierarchy of levels for Sunburst or Treemap charts.

        Levels are given starting from the bottom to the top of the hierarchy,
        ie the last level corresponds to the root.
        """
        df_all_trees = pd.DataFrame(columns=['id', 'parent', 'value', 'color'])
        for i, level in enumerate(levels):
            df_tree = pd.DataFrame(columns=['id', 'parent', 'value', 'color'])
            dfg = df.groupby(levels[i:]).sum()
            dfg = dfg.reset_index()
            df_tree['id'] = dfg[level].copy()
            if i < len(levels) - 1:
                df_tree['parent'] = dfg[levels[i+1]].copy()
            else:
                df_tree['parent'] = 'total'
            df_tree['value'] = dfg[value_column]
            df_tree['color'] = dfg[color_columns[0]]
            df_all_trees = df_all_trees.append(df_tree, ignore_index=True)
        total = pd.Series(dict(id='total', parent='',
            value=df[value_column].sum(),
            color=df[color_columns[0]].sum()))
        df_all_trees = df_all_trees.append(total, ignore_index=True)
        return df_all_trees


    TERMINAL = True

    """
    # --------------------------------------------------------------------
    #                               Main
    # --------------------------------------------------------------------
    # Load data
    data, antimicrobials, microorganisms = load_data_nhs(nrows=10000)

    # Create DataFrame
    dataframe = data.groupby(['specimen_code',
                              'microorganism_code',
                              'antimicrobial_code',
                              'sensitivity']) \
                    .size().unstack().fillna(0)

    # Compute frequency
    dataframe['freq'] = dataframe.sum(axis=1)

    # Compute sari
    dataframe['sari'] = sari(dataframe, strategy='hard')
    dataframe['sari_medium'] = sari(dataframe, strategy='medium')
    dataframe['sari_soft'] = sari(dataframe, strategy='soft')

    # Reset index
    dataframe = dataframe.reset_index()

    # --------------------------------------------
    # Add info for popup
    # --------------------------------------------
    dataframe = dataframe.merge(antimicrobials,
        how='left', left_on='antimicrobial_code',
        right_on='antimicrobial_code')

    # Add antimicrobials information
    dataframe = dataframe.merge(microorganisms,
        how='left', left_on='microorganism_code',
        right_on='microorganism_code')

    # Format dataframe
    dataframe = dataframe.round(decimals=3)

    # Replace
    dataframe.microorganism_name = \
        dataframe.microorganism_name.str.title()
    dataframe.columns = \
        dataframe.columns.str.title().str.replace('_', ' ')


    # Show
    if TERMINAL:
        print("\nColumns:")
        print(dataframe.dtypes)
        print("\nDF:")
        print(dataframe)


    # -------------------------------------------
    # Plot
    # -------------------------------------------
    def guide_template(names):
        return '<br>'.join([
            "%2d <b>%-45s</b> %%{customdata[%s]}" % (i, n, i )
                for i, n in enumerate(names)])

    # Guide template
    htmp_guide = guide_template(dataframe.columns.tolist())

    # Define own template
    htmp = "Specimen:      (%{customdata[0]})<br>"
    htmp+= "Microorganism: %{customdata[26]} (%{customdata[1]})<br>"
    htmp+= "Antimicrobial: %{customdata[12]} (%{customdata[2]})<br>"
    htmp+= "Freq: %{customdata[8]}<br>"
    htmp+= "SARI: %{customdata[9]}<br>"

    htmp = "(%{customdata[0]})<br>"
    htmp+= "%{customdata[26]} (%{customdata[1]})<br>"
    htmp+= "%{customdata[12]} (%{customdata[2]})<br>"
    htmp+= "Freq: %{customdata[8]}<br>"
    htmp+= "SARI: %{customdata[9]}<br>"

    # Display
    fig = px.treemap(dataframe,
        path=['Specimen Code',
              'Microorganism Code',
              'Antimicrobial Code'],
        #hover_name=,
        hover_data=dataframe.columns.tolist(),
        values='Freq',
        color='Sari',
        color_continuous_scale='Reds',
        title='Treemap of <Microorganisms, Antimicrobials> pairs')


    # Show current template
    print(fig.data[0].hovertemplate)
    """

    """
    The default hover template looks as follows:

        labels=%{label}<br>
        Freq=%{value}<br>
        parent=%{parent}<br>
        id=%{id}<br>
        Microorganism Name=%{customdata[0]}<br>
        Name=%{customdata[1]}<br>
        Sari Medium=%{customdata[2]}<br>
        Sari Soft=%{customdata[3]}<br>
        Sari=%{color}
        <extra></extra>
    """

    """
    # Set custom data (not needed and inconsistent)
    #fig.data[0].customdata = dataframe.to_numpy()
    #fig.data[0].hovertemplate = htmp

    # Uncomment to check the customdata[i] information
    #fig.data[0].hovertemplate = \
    #    guide_template(dataframe.columns.tolist())

    # Update: I
    #fig.update_traces(hovertemplate='labels=%{label}')
    #fig.update_traces(texttemplate='Freq=%{value:.2f}<br>')
    fig.update_traces(hovertemplate=htmp_guide)
    #fig.update_traces(hovertemplate=htmp)

    # Update: II
    # But it seems to me you want something like
    #fig.data[0].hovertemplate = '%{label}<br>%{value}'
    #fig.data[0].hovertemplate = '%{Freq}<br>%{Antimicrobial Name}'

    fig.update_layout(
        margin={
            'l': 0,
            'r': 0,
            'b': 0,
            't': 0,
            'pad': 4
         })
    # ----------------------------
    # Save
    # ----------------------------
    # Libraries
    import time
    from pathlib import Path

    # Define pipeline path
    path = Path('./objects') / 'plot_main08_treemap'
    filename = '%s.html' % time.strftime("%Y%m%d-%H%M%S")

    # Create folder (if it does not exist)
    path.mkdir(parents=True, exist_ok=True)

    # Save
    fig.write_html("%s/%s" % (path, filename))

    # Show
    show(fig)
    """

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

   **Total running time of the script:** ( 0 minutes  0.099 seconds)


.. _sphx_glr_download__examples_plotly_main06_treemap_v3.py:


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



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

     :download:`Download Python source code: main06_treemap_v3.py <main06_treemap_v3.py>`



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     :download:`Download Jupyter notebook: main06_treemap_v3.ipynb <main06_treemap_v3.ipynb>`


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