.. _sphx_glr_auto_examples_plot_normalize.py:


=============================
Normalizing your features
=============================

Often times its useful to normalize (z-score) you features before plotting, so
that they are on the same scale.  Otherwise, some features will be weighted more
heavily than others when doing PCA, and that may or may not be what you want.
The `normalize` kwarg can be passed to the plot function.  If `normalize` is
set to 'across', the zscore will be computed for the column across all of the
lists passed.  Conversely, if `normalize` is set to 'within', the z-score will
be computed separately for each column in each list.  Finally, if `normalize` is
set to 'row', each row of the matrix will be zscored.  Alternatively, you can use
the normalize function found in tools (see the third example).




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


    *

      .. image:: /auto_examples/images/sphx_glr_plot_normalize_001.png
            :scale: 47

    *

      .. image:: /auto_examples/images/sphx_glr_plot_normalize_002.png
            :scale: 47

    *

      .. image:: /auto_examples/images/sphx_glr_plot_normalize_003.png
            :scale: 47





.. code-block:: python


    # Code source: Andrew Heusser
    # License: MIT

    # import
    import hypertools as hyp
    import numpy as np
    import matplotlib.pyplot as plt

    # simulate data
    cluster1 = np.random.multivariate_normal(np.zeros(3), np.eye(3), size=100)
    cluster2 = np.random.multivariate_normal(np.zeros(3)+10, np.eye(3), size=100)
    data = [cluster1, cluster2]

    # plot normalized across lists
    hyp.plot(data, '.', normalize='across', title='Normalized across datasets')

    # plot normalized within list
    hyp.plot(data, '.', normalize='within', title='Normalized within dataset')

    # normalize by row
    normalized_row = hyp.normalize(data, normalize='row')

    # plot normalized by row
    hyp.plot(normalized_row, '.', title='Normalized across row')

**Total running time of the script:** ( 0 minutes  0.211 seconds)



.. only :: html

 .. container:: sphx-glr-footer


  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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