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

    Click :ref:`here <sphx_glr_download_auto_examples_NeoAll_examples_plot_neoAll_ex2.py>` to download the full example code
.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_NeoAll_examples_plot_neoAll_ex2.py:


===========================
Neo All - example 2 - Cross-Correlograms
===========================

This example shows how to compute and plot cross-correlograms of spiketrains from different units.

.. note:: The crosscorrelogram compares the output of 2 different neurons, it indicates the firing rate of one neuron
          versus another. See `here <https://www.med.upenn.edu/mulab/crosscorrelation.html>`_ for more details

.. image:: ./../../_static/images/crosscorrelogram.png




First import neoStructures



.. code-block:: python

    from neoStructures import *
    import matplotlib.pyplot as plt
    from os.path import isdir, join







Import the data and create the NeoAll instance



.. code-block:: python

    data_dir = join('pySpikeAnalysis', 'sample_data') if isdir('pySpikeAnalysis') else join('..', '..', 'pySpikeAnalysis', 'sample_data')
    spykingcircus_dir = r'SpykingCircus_results'
    probe_filename = r'000_AA.prb'
    results_filename = r'spykingcircusres'

    neoAll = NeoAll(join(data_dir, spykingcircus_dir), results_filename, join(data_dir, probe_filename), save_fig=0)







See information about NeoAll



.. code-block:: python

    print(neoAll)





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

 Out:

 .. code-block:: none

    NeoAll Instance with 54 units. 1 Neo segment per unit. Each segment contains 1 Neo spiketrain
    10 channel indexes


Use :func:`neoStructures.NeoAll.plot_crosscorrelogram` to plot cross-correlogram between 2 units. The spiketrains are first converted into binned
spiketrains before the computation of the cross-correlogram.
The package `Elephant <http://elephant.readthedocs.io/en/latest/index.html>`_ is used for the binning as well as for computing
the cross-correlogram.
Let's compute the cross-correlogram between the first 2 units :



.. code-block:: python

    neoAll.plot_crosscorrelogram(0, 1)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_001.png
    :class: sphx-glr-single-img




We can see from these cross-correlogram that the two units often fire together
Bin duration is set by default to 1ms but can be modified. The max_lag_time parameter sets the time limits of the
cross-correlogram, its default value is set to 80 ms
It can be changed to zoom on the peak near the origin :



.. code-block:: python

    neoAll.plot_crosscorrelogram(0, 1, bin_time=1*ms, max_lag_time=25*ms)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_002.png
    :class: sphx-glr-single-img




Some statistics can be computed, be setting the do_stat parameter to 1 : n_surrogates spike-trains are created
in which a jitter is added to the time of the spikes. The jitter is computed from a normal distribution whose standard
deviation is fixed by the normal_dist_sd parameter. The 99% confidence interval computed from the jittered spiketrains
is shown on top of the cross-correlogram.



.. code-block:: python

    neoAll.plot_crosscorrelogram(0, 1, do_stat=True, n_surrogates=20, normal_dist_sd=25*ms)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_003.png
    :class: sphx-glr-single-img




If unit_pos_a and unit_pos_b parameters are equals, the autocorrelogram is computed.



.. code-block:: python

    neoAll.plot_crosscorrelogram(0, 0)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_004.png
    :class: sphx-glr-single-img




Multiples cross-correlogram can be plot at the same time in multiple figures :



.. code-block:: python

    neoAll.plot_crosscorrelogram(0, [0, 1, 2])




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


    *

      .. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_005.png
            :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_006.png
            :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_007.png
            :class: sphx-glr-multi-img




Or in the same figure :



.. code-block:: python

    neoAll.plot_crosscorrelogram([0, 1, 2], [0, 1, 2], merge_plots=1)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_008.png
    :class: sphx-glr-single-img




If same_yscale is True, the cross-correlograms are smoothed and the same y-scale is used.



.. code-block:: python

    neoAll.plot_crosscorrelogram([0, 1, 2], [0, 1, 2], merge_plots=1, same_yscale=1, fill_under_plot=1)






.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_neoAll_ex2_009.png
    :class: sphx-glr-single-img




**Total running time of the script:** ( 0 minutes  6.766 seconds)


.. _sphx_glr_download_auto_examples_NeoAll_examples_plot_neoAll_ex2.py:


.. only :: html

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



  .. container:: sphx-glr-download

     :download:`Download Python source code: plot_neoAll_ex2.py <plot_neoAll_ex2.py>`



  .. container:: sphx-glr-download

     :download:`Download Jupyter notebook: plot_neoAll_ex2.ipynb <plot_neoAll_ex2.ipynb>`


.. only:: html

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

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