Plotting Figures

The backend for generating plots for Neuroblox is Makie. In order to call these functions, one must have a Makie backend installed, such as CairoMakie or GLMakie.

NeurobloxBase.meanfield — Function
meanfield(blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution)

Plot the mean-field voltage (in mV) as a function of time (in ms) for a blox.

Arguments:

  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Note: this function requires Makie to be loaded.

See also meanfield!, meanfield_timeseries.

NeurobloxBase.meanfield! — Function
meanfield!(ax::Axis, blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol)

Update an existing plot Axis to show the mean-field voltage (in mV) as a function of time (in ms) for a blox.

Arguments:

  • ax : an Axis object attached to a Figure from Makie.
  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Note: this function requires Makie to be loaded.

See also meanfield, meanfield_timeseries.

NeurobloxBase.rasterplot — Function
rasterplot(blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution; threshold = nothing, kwargs...)

Create a scatterplot of spikes, where the x-axis is time (in ms) and the y-axis represents neurons organized in separate rows.

Arguments:

  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • threshold : [mV] Spiking threshold. Internally used in detect_spikes to calculate all spiking events. Note that neurons like NeurobloxPharma.HHNeuronExci and NeurobloxPharma.HHNeuronInhib do not inherently contain a threshold and so require this threshold argument to be passed in order to determine spiking events.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

Note: this function requires Makie to be loaded.

See also rasterplot!, detect_spikes.

NeurobloxBase.rasterplot! — Function
rasterplot!(ax::Axis, blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution; threshold = nothing, kwargs...)

Update an existing plot Axis to show a scatterplot of spikes, where the x-axis is time (in ms) and the y-axis represents neurons organized in separate rows.

Arguments:

  • ax : an Axis object attached to a Figure from Makie.
  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • threshold : [mV] Spiking threshold. Internally used in detect_spikes to calculate all spiking events. Note that neurons like NeurobloxPharma.HHNeuronExci and NeurobloxPharma.HHNeuronInhib do not inherently contain a threshold and so require this threshold argument to be passed in order to determine spiking events.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

Note: this function requires Makie to be loaded.

See also rasterplot, detect_spikes.

NeurobloxBase.stackplot — Function
stackplot(blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution)

Plot the voltage timeseries of all neurons contained in blox, stacked on top of each other. The x-axis is time (in ms) and on the y-axis voltage timeseries are plotted on separate rows for each neuron in blox.

Arguments:

  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Note: this function requires Makie to be loaded.

See also stackplot!.

NeurobloxBase.stackplot! — Function
stackplot!(ax::Axis, blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution)

Update an existing plot Axis to show the voltage timeseries of all neurons contained in blox, stacked on top of each other. The x-axis is time (in ms) and on the y-axis voltage timeseries are plotted on separate rows for each neuron in blox.

Arguments:

  • ax : an Axis object attached to a Figure from Makie.
  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Note: this function requires Makie to be loaded.

See also stackplot.

NeurobloxBase.frplot — Function
frplot(blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution; win_size = 10, overlap = 0, transient = 0, threshold = nothing, kwargs...)

Plot the firing rate of blox as a function of time (in s).

Arguments:

  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons. If blox contains more than one neurons, then the average firing rate across all neurons is plotted.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • win_size : [ms] Sliding window size.
  • overlap : in range [0,1]. Overlap between two consecutive sliding windows.
  • transient : [ms] Transient period in the beginning of the timeseries that is ignored during firing rate calculation.
  • threshold : [mV] Spiking threshold.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

win_size, overlap, transient and threshold are internally used in firing_rate to calculate the firing rate timeseries.

Note: this function requires Makie to be loaded.

See also frplot!, firing_rate.

NeurobloxBase.frplot! — Function
frplot!(ax::Axis, blox::Union{AbstractComposite, Vector{AbstractNeuron}}, sol::AbstractSolution; win_size = 10, overlap = 0, transient = 0, threshold = nothing, kwargs...)

Update an existing plot Axis to show the firing rate of blox as a function of time (in s).

Arguments:

  • ax : an Axis object attached to a Figure from Makie.
  • blox : a composite blox, e.g. a brain region or microcircuit, containing multiple neurons or a vector of neurons. If blox contains more than one neurons, then the average firing rate across all neurons is plotted.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • win_size : [ms] Sliding window size.
  • overlap : in range [0,1]. Overlap between two consecutive sliding windows.
  • transient : [ms] Transient period in the beginning of the timeseries that is ignored during firing rate calculation.
  • threshold : [mV] Spiking threshold.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

win_size, overlap, transient and threshold are internally used in firing_rate to calculate the firing rate timeseries.

Note: this function requires Makie to be loaded.

See also frplot, firing_rate.

NeurobloxBase.powerspectrumplot — Function
powerspectrumplot(blox::Union{AbstractComposite, Vector{Union{AbstractNeuron, AbstractNeuralMass}}, sol::AbstractSolution; sampling_rate=nothing, method=periodogram, window=nothing, kwargs...)

Plot the power spectrum (intensity as a function of frequency) of neurons and neural mass objects contained in blox.

Arguments:

  • blox : a composite blox, e.g. a brain region or microcircuit, or a vector containing multiple neurons and/or neural masses.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • sampling_rate : [Hz] Sampling rate.
  • method : Method to calculate the periodogram. Options are [periodogram, welch_pgram]. See the DSP documentation for more information.
  • window : An optional window function to be applied to the original signal before computing the Fourier transform. Options are [nothing, hamming, hanning]. See the DSP documentation for more information.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

Note: this function requires Makie to be loaded.

See also powerspectrumplot!, powerspectrum.

NeurobloxBase.powerspectrumplot! — Function
powerspectrumplot!(ax::Axis, blox::Union{AbstractComposite, Vector{Union{AbstractNeuron, AbstractNeuralMass}}, sol::AbstractSolution; sampling_rate=nothing, method=periodogram, window=nothing, kwargs...)

Update an existing plot Axis to show the power spectrum (intensity as a function of frequency) of neurons and neural mass objects contained in blox.

Arguments:

  • ax : an Axis object attached to a Figure from Makie.
  • blox : a composite blox, e.g. a brain region or microcircuit, or a vector containing multiple neurons and/or neural masses.
  • sol : a solution object after running a simulation (i.e. the output of solve)

Keyword arguments:

  • sampling_rate : [Hz] Sampling rate.
  • method : Method to calculate the periodogram. Options are [periodogram, welch_pgram]. See the DSP documentation for more information.
  • window : An optional window function to be applied to the original signal before computing the Fourier transform. Options are [nothing, hamming, hanning]. See the DSP documentation for more information.
  • kwargs... : All other keyword arguments are passed to Makie to control figure properties.

Note: this function requires Makie to be loaded.

See also powerspectrumplot, powerspectrum.