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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_plot_ttest.py:


Tutorial 03: Plot of mean and statistical data (t-test)
=======================================================
Example script to plot both mean data and statistics, e.g. from paired or unpaied t-test with two groups.

.. GENERATED FROM PYTHON SOURCE LINES 6-51







.. code-block:: Python

    from surface_plot import plot_mean_stats
    import numpy as np

    outdir = 'data/paired_ttest/test_figures'
    clobber = False

    # Load data
    pval_left = np.loadtxt('https://www.dropbox.com/s/5g3sopvolf0qnot/left.pval?dl=1', skiprows=1)
    pval_right = np.loadtxt('https://www.dropbox.com/s/282xfgqk4wx2pka/right.pval?dl=1', skiprows=1)
    tval_left = np.loadtxt('https://www.dropbox.com/s/ku6wdm4nd8690rg/left.tval?dl=1', skiprows=1)
    tval_right = np.loadtxt('https://www.dropbox.com/s/oci987u02nwtgxf/right.tval?dl=1', skiprows=1)

    mean1_left = np.loadtxt('https://www.dropbox.com/s/htx0q2lm87nnlf1/baseline_left.mean?dl=1', skiprows=1)
    mean1_right = np.loadtxt('https://www.dropbox.com/s/mbe1a3v8vtgrlsx/baseline_right.mean?dl=1', skiprows=1)
    mean2_left = np.loadtxt('https://www.dropbox.com/s/f71pewt2748dag7/followup_left.mean?dl=1', skiprows=1)
    mean2_right = np.loadtxt('https://www.dropbox.com/s/8r8jfkqz9rxjrr3/followup_right.mean?dl=1', skiprows=1)

    tval = {'left': tval_left,
            'right': tval_right}

    pval = {'left': pval_left,
            'right': pval_right}

    mean1 = {'left': mean1_left,
                'right': mean1_right}

    mean2 = {'left': mean2_left,
                'right': mean2_right}

    # Define statistical threshold
    p_threshold = 0.01

    # P value
    output = f'{outdir}/ttest_pval_p{p_threshold}.pdf'
    plot_mean_stats.plot_mean_stats(mean1, mean2, tval, output, pval=pval, vlim=[0, 4], p_threshold=p_threshold, cb_mean_title='Mean SUVR', mean_titles=['Baseline', 'Follow-up'], stats_titles=['Increase', 'Decrease'], clobber=clobber)

    output = f'{outdir}/ttest_pval_notitle_p{p_threshold}.pdf'
    plot_mean_stats.plot_mean_stats(mean1, mean2, tval, output, pval=pval, vlim=[0, 4], p_threshold=p_threshold, clobber=clobber)

    # T value
    output = f'{outdir}/ttest_tval_p{p_threshold}.pdf'
    plot_mean_stats.plot_mean_stats(mean1, mean2, tval, output, vlim=[0, 4], pval=pval, p_threshold=p_threshold, cb_mean_title='Mean SUVR', mean_titles=['Baseline', 'Follow-up'], stats_titles=['Change'], plot_tvalue=True, clobber=clobber)

    output = f'{outdir}/ttest_tval_notitle_p{p_threshold}.pdf'
    plot_mean_stats.plot_mean_stats(mean1, mean2, tval, output, pval=pval, vlim=[0, 4], p_threshold=p_threshold, plot_tvalue=True, clobber=clobber)


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

   **Total running time of the script:** (0 minutes 16.165 seconds)


.. _sphx_glr_download_auto_examples_plot_ttest.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_ttest.zip <plot_ttest.zip>`


.. only:: html

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

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