Visualize Rate Statistics of CBGTC spike times¶

Rate Plotting¶

Functions
`plot_mean_rate_isi()`
`plot_mean_rate_isi_in_ax()`
`plot_pool_avg_inst_rates()`
`plot_pool_avg_inst_rates_in_ax()`
`plot_true_avg_inst_rate()`
`plot_true_avg_inst_rate_in_ax()`
`plot_mean_rate_spikecounts_in_ax()`
`plot_mean_rate_all_neurons_across_time_in_ax()`

Plot Mean Rate¶

1. Pre-requisites¶

1.1. Import Modules¶

from analyseur.cbgtc.loader import LoadSpikeTimes
from analyseur.cbgtc.visual.rate import plot_mean_rate_isi

1.2. Load file and get spike times¶

loadST = LoadSpikeTimes("spikes_GPi.csv")
spiketimes_superset = loadST.get_spiketimes_superset()

2. Cases¶

2.1. Visualize Mean Rate with default setting¶

[fig, ax] = plot_mean_rate_isi(spiketimes_superset)

2.2. Visualize Mean Rate in portrait mode¶

[fig, ax] = plot_mean_rate_isi(spiketimes_superset, mode="portrait")

2.3. Visualize Mean Rate in portrait mode with nucleus name in title¶

[fig, ax] = plot_mean_rate_isi(spiketimes_superset, mode="portrait", nucleus="GPi")

2.4. Create the plot for customization¶

This is for power users who for instance want to insert the Mean Rate plot in their collage of subplots.

import matplotlib.pyplot as plt
from analyseur.cbgtc.visual.rate import plot_mean_rate_isi_in_ax

fig, (ax1, ax2) = plt.subplots(1, 2)
fig.suptitle('Horizontally stacked subplots')

ax1 = plot_mean_rate_isi_in_ax(ax1, spiketimes_superset)
ax2 = plot_mean_rate_isi_in_ax(ax2, spiketimes_superset)

plt.show()

NOTE: This example shows plot_mean_rate_isi_in_ax() in default setting but this function works like plot_mean_rate_isi() therefore all the cases 2.1, 2.2 and 2.3 are applicable for plot_mean_rate_isi_in_ax().

Plot Average Instantaneous Rate¶

Similar as documented above for plotting Mean Rate but using the function plot_avg_inst_rate() and plot_avg_inst_rate_in_ax() with the additional OPTIONAL argument for binsz (otherwise it picks a default value). This is imported as

from analyseur.cbgtc.visual.rate import plot_avg_inst_rate, plot_avg_inst_rate_in_ax

analyseur.cbgtc.visual.rate.plot_mean_rate_all_neurons_across_time_in_ax(ax, spiketimes_set, window=None, binsz=None, nucleus=None)[source]¶

Mean Population Firing Rate Over Time

Firing Rate (Hz)
^
|        ~~~      ~~~    ~~~        ~~~
|      ~~   ~~  ~~   ~~  ~~   ~~  ~~   ~~
|     ~      ~~       ~~      ~~       ~
|
+--------------------------------------------------> Time (s)
0        5        10        15        20

Line shows the mean firing rate of the neuron population
as it evolves over time.

Draws the Mean Firing Rate (1/s) over time on the given matplotlib.pyplot.axis

Parameters:

ax – object matplotlib.pyplot.axis`
spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

OPTIONAL parameters

Parameters:

window – 2-tuple; (0, 10) [default]
binsz – 0.01 [default]
nucleus – string; name of the nucleus

Returns:

object ax with plotting of the temporal dynamics of the mean firing rate across neurons

analyseur.cbgtc.visual.rate.plot_mean_rate_isi(spiketimes_superset, nucleus=None, mode=None)[source]¶

Visualize Mean Rate (1/s) of the given neuron population using plot_mean_rate_isi_in_ax().

Parameters:: spiketimes_superset – Dictionary returned using analyseur.cbgtc.stats.isi.InterSpikeInterval.compute()

OPTIONAL parameters

param nucleus:

string; name of the nucleus
param mode:

“portrait” or None/landscape [default]
return:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_mean_rate_isi_in_ax(ax, spiketimes_set, nucleus=None, mode=None)[source]¶

Mean Rate (1/s)
^
|      █  █   █ █   █   █ █   █
|     ███ ██ ████ ██ ██ ███ ██
|    █████████████████████████
|
+---------------------------------------------> Neurons
0      50      100      150      200

Each bar represents the mean firing rate of one neuron
computed from its inter-spike intervals (ISI).

Draws the Mean Rate (1/s) on the given matplotlib.pyplot.axis

Parameters:

ax – object matplotlib.pyplot.axis`
spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

OPTIONAL parameters

param nucleus:

string; name of the nucleus
param mode:

“portrait” or None/landscape [default]
return:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_mean_rate_spikecounts_in_ax(ax, spiketimes_set, window=None, binsz=None, nucleus=None, mode=None)[source]¶

Mean Rate (1/s)
^
|      █  █   █ █   █   █ █   █
|     ███ ██ ████ ██ ██ ███ ██
|    █████████████████████████
|
+---------------------------------------------> Neurons
0      50      100      150      200

Each bar represents the mean firing rate of one neuron
computed from spike counts within the analysis window.

Draws the Mean Rate (1/s) on the given matplotlib.pyplot.axis

Parameters:

ax – object matplotlib.pyplot.axis`
spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

OPTIONAL parameters

param nucleus:

string; name of the nucleus
param mode:

“portrait” or None/landscape [default]
return:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_pool_avg_inst_rates(spiketimes_superset, binsz=None, nucleus=None, mode=None)[source]¶

Visualize Mean Rate (1/s) of the given neuron population using plot_pool_avg_inst_rates_in_ax().

Parameters:: spiketimes_superset – Dictionary returned using LoadSpikeTimes

OPTIONAL parameters

param binsz:

0.01 [default]
param nucleus:

string; name of the nucleus
param mode:

“portrait” or None/landscape [default]
return:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_pool_avg_inst_rates_in_ax(ax, spiketimes_superset, binsz=None, nucleus=None, mode=None)[source]¶

Average Inst. Rate (Hz)
^
|      ███ ████ ███ ████ ███ ███
|     █████████████████████████
|    ██████████████████████████
|
+--------------------------------------------------> Time (s)
0        2        4        6        8        10

Each bar represents the average instantaneous firing rate
of the neuron population within a time bin.

Draws the Mean Rate (1/s) on the given matplotlib.pyplot.axis

Parameters:

ax – object matplotlib.pyplot.axis`
spiketimes_superset – Dictionary returned using analyseur.cbgtc.stats.isi.InterSpikeInterval.compute()

OPTIONAL parameters

param binsz:

0.01 [default]
param nucleus:

string; name of the nucleus
param mode:

“portrait” or None/landscape [default]
return:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_true_avg_inst_rate(spiketimes_set, nucleus=None, mode=None)[source]¶

Visualize Instantaneuous Rate (1/s) of the given neuron population using plot_true_avg_inst_rate_in_ax().

Parameters:: spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

OPTIONAL parameters

Parameters:

neurons –
“all” or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]
- ”all” means subset = superset
- N (a scalar) means subset of first N neurons in the superset
- range(a, b) or [2, 3, 6, 7] means subset of selected neurons
nucleus – string; name of the nucleus
mode – “portrait” or None/landscape [default]

Returns:

object ax with Rate Distribution plotting done into it

analyseur.cbgtc.visual.rate.plot_true_avg_inst_rate_in_ax(ax, spiketimes_set, nucleus=None, mode=None)[source]¶

Avg. Inst. Rate (Hz)
^
|      █  █   █ █   █   █ █   █
|     ███ ██ ████ ██ ██ ███ ██
|    █████████████████████████
|
+---------------------------------------------> Neurons
0      50      100      150      200

Each bar represents the average instantaneous firing rate
of an individual neuron computed from its ISI sequence.

Draws the Instantaneuous Rate (1/s) on the given matplotlib.pyplot.axis

Parameters:

ax – object matplotlib.pyplot.axis`
spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

OPTIONAL parameters

Parameters:

neurons –
“all” or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]
- ”all” means subset = superset
- N (a scalar) means subset of first N neurons in the superset
- range(a, b) or [2, 3, 6, 7] means subset of selected neurons
nucleus – string; name of the nucleus
mode – “portrait” or None/landscape [default]

Returns:

object ax with Rate Distribution plotting done into it