cibrrig.analysis.singlecell
===========================

.. py:module:: cibrrig.analysis.singlecell


Functions
---------

.. autoapisummary::

   cibrrig.analysis.singlecell.get_phase_curve
   cibrrig.analysis.singlecell.get_all_phase_curves


Module Contents
---------------

.. py:function:: get_phase_curve(ts, breaths, phi_t=None, phi=None, nbins=100)

   Computes the firing rate of a neuron for a given respiratory phase.

   The computation is done on a per-breath basis to obtain a distribution.

   :param ts: Times of spikes for a single neuron.
   :type ts: array-like
   :param breaths: Breath segments.
   :type breaths: array-like
   :param phi_t: Time basis of the phase variable `phi`.
   :type phi_t: array-like
   :param phi: Respiratory phase at a given time.
   :type phi: array-like
   :param nbins: Number of bins in the phasic PSTH. Defaults to 100.
   :type nbins: int, optional

   :returns:

             A dictionary with the following keys:
                 - bins (array-like): Bin edges.
                 - rate_mean (array-like): Mean firing rate.
                 - rate_std (array-like): Standard deviation of the firing rate.
                 - rate_sem (array-like): Standard error of the mean firing rate.
   :rtype: dict


.. py:function:: get_all_phase_curves(spike_times, spike_clusters, cluster_ids, breaths, nbins=100)

   Computes the firing rate of all neurons in `cluster_ids` for a given respiratory phase.

   The computation is done on a per-breath basis to obtain a distribution.

   :param spike_times: Times of spikes for all neurons.
   :type spike_times: array-like
   :param spike_clusters: Cluster assignment of spikes for all neurons.
   :type spike_clusters: array-like
   :param cluster_ids: IDs of clusters to analyze.
   :type cluster_ids: array-like
   :param breaths: Breath segments.
   :type breaths: array-like
   :param nbins: Number of bins in the phasic PSTH. Defaults to 100.
   :type nbins: int, optional

   :returns: Bin edges.
             - rate (array-like): Firing rate, shape [nbins x n_cluster_ids].
             - sem (array-like): Standard error of the mean, shape [nbins x n_cluster_ids].
             - raster (array-like): Raster data.
             - rate_sem (array-like): SEM of the raster rate, shape [nbins x n_cluster_ids].
   :rtype: - bins (array-like)