cibrrig.plot

Attributes

has_brainbox
laser_colors

Functions

plot_laser(laser_in, **kwargs)	Flexibly overlay laser stimulation.
_plot_laser_alf(laser_in, **kwargs)	Plot laser data from a "laser" AlfBunch.
_plot_laser_intervals(intervals[, amplitudes, ax, ...])	Plot laser intervals from arrays.
_plot_laser_log(log[, query, rotation, fontsize])	Plot laser data from a "log" AlfBunch object.
_create_ax(dims[, projection])	Create a new figure and axis.
_setup_colorbar(ax, p, vmin, vmax, colorbar_title)	Set up a colorbar for the plot.
plot_projection_line_multicondition(X, tbins, ...[, ...])	Plot low-D projection with unique coloring for the given intervals.
plot_projection_line(X[, cvar, dims, cmap])	Plot low-d projection as a line. Optionally
_plot_projection_line_2D(X[, cvar, dims, cmap, color, ...])	Plot 2D projection line.
_plot_projection_line_3D(X[, cvar, dims, cmap, color, ...])	Plot 3D projection line.
plot_projection(X, dims, **kwargs)	Plot projection in 2D or 3D.
plot_3D_projection(X[, dims, cvar, ax, title, s, ...])	Plot 3D projection.
plot_2D_projection(X[, dims, cvar, ax, title, s, ...])	Plot 2D projection.
plot_polar_average(x, y, t[, ax, t0, tf, color, bins, ...])	Plot covariate y as a function of phase x on a polar.
plot_reset_curve(breaths, events[, wavelength, ...])	Plot a reset curve for optogenetic stimulation, showing phase-dependent effects on breathing cycles.
plot_sweeps(xt, x, times, pre, post[, ax])	Time-aligns a trace x to event times specified in times.
plot_most_likely_dynamics(model[, xlim, ylim, nxpts, ...])	Plotting of underlying vector fields from Linderman Lab
plot_most_likely_dynamics_3D(model[, xlim, ylim, ...])	Extension of the linderman vectorfield plot to 3D
_clean_3d_axes(ax, title, dims, pane_color[, lims])	Modify 3D axes to be cleaner:
clean_polar_axis(ax)	Clean the appearance of a polar plot.
clean_linear_radial_axis(ax)	Clean the appearance of a plot with a range o [-pi,pi] but on a normal, linear axis
plot_driftmap_with_trace(spike_times, spike_depths, ...)	#TODO: Update documentation
replace_timeaxis_with_scalebar(ax[, pad, lw, color, size])	Replace the x-axis with a horizontal bar showing the time scale of the plot.
trim_yscale_to_lims(ax, ymin, ymax)
plot_peth_and_raster(spike_times, starts[, stops, ...])	Plot a peri-event time histogram and raster plot

Module Contents

cibrrig.plot.has_brainbox = True

cibrrig.plot.laser_colors

cibrrig.plot.plot_laser(laser_in, **kwargs)

Flexibly overlay laser stimulation.

Parameters:

• laser_in (AlfBunch or array-like) – The laser data to be plotted. Can be an AlfBunch object or an array of intervals.

• **kwargs – Additional keyword arguments to be passed to the plotting functions. These may include: mode (str): The plotting mode. Options are “shade”, “bar”, “vline”, or any other (defaults to steps). ax (matplotlib.axes.Axes): The axes object to plot on. If None, a new figure and axes will be created. amp_label (str): Label for the amplitude axis when plotting amplitudes. wavelength (int): Laser wavelength in nm, used to determine the color of the plot. alpha (float or array-like): The alpha (transparency) value(s) for shaded areas. color (str or tuple): The color to use for plotting. If not provided, a default color based on wavelength is used. query (str): Query string to filter the data (only used in _plot_laser_log). rotation (int): Rotation angle for text annotations (only used in _plot_laser_log). fontsize (int): Font size for text annotations (only used in _plot_laser_log). Any other keyword arguments accepted by matplotlib plotting functions.

Returns:

The axes object containing the plot.

Return type:

matplotlib.axes.Axes

Notes

This function determines the appropriate plotting method based on the input type: - If laser_in is an AlfBunch object with a ‘category’ key, it calls _plot_laser_log. - If laser_in is an AlfBunch object without a ‘category’ key, it calls _plot_laser_alf. - For other input types, it calls _plot_laser_intervals.

The specific kwargs used may vary depending on which underlying plotting function is called.

cibrrig.plot._plot_laser_alf(laser_in, **kwargs)

Plot laser data from a “laser” AlfBunch.

Parameters:

• laser_in (AlfBunch) – The AlfBunch object containing laser data.

• **kwargs – Additional keyword arguments to be passed to _plot_laser_intervals.

Notes

This function extracts intervals and amplitudes from the AlfBunch object and calls _plot_laser_intervals with the appropriate parameters. It determines whether to use milliwatts or volts for the amplitude label based on the available keys in laser_in.

cibrrig.plot._plot_laser_intervals(intervals, amplitudes=None, ax=None, mode='shade', amp_label='', wavelength=473, alpha=0.2, **kwargs)

Plot laser intervals from arrays.

Parameters:

• intervals (array-like) – Array of laser intervals, where each interval is [start_time, end_time].

• amplitudes (array-like, optional) – Array of amplitude values corresponding to each interval.

• ax (matplotlib.axes.Axes, optional) – The axes object to plot on. If None, a new figure and axes will be created.

• mode (str, optional) – The plotting mode. Options are “shade”, “bar”, “vline”, or any other (defaults to steps).

• amp_label (str, optional) – Label for the amplitude axis when plotting amplitudes.

• wavelength (int, optional) – Laser wavelength in nm, used to determine the color of the plot. Default is 473.

• alpha (float or array-like, optional) – The alpha (transparency) value(s) for shaded areas. Default is 0.2.

• **kwargs – Additional keyword arguments to be passed to the plotting functions.

Returns:

The axes object containing the plot.

Return type:

matplotlib.axes.Axes

Notes

This function supports multiple plotting modes: - “shade”: Shades the intervals on the plot. - “bar”: Plots horizontal bars for each interval. - “vline”: Plots vertical lines at the start of each interval. - Any other mode defaults to plotting steps of the amplitudes.

The function handles color selection based on the wavelength and can use a list of alpha values for varying transparency across intervals.

cibrrig.plot._plot_laser_log(log, query=None, rotation=45, fontsize=6, **kwargs)

Plot laser data from a “log” AlfBunch object.

Parameters:

• log (AlfBunch) – The AlfBunch object containing laser log data.

• query (str, optional) – Query string to filter the data. Default is None.

• rotation (int, optional) – Rotation angle for text annotations. Default is 45.

• fontsize (int, optional) – Font size for text annotations. Default is 6.

• **kwargs – Additional keyword arguments to be passed to _plot_laser_intervals.

Returns:

The axes object containing the plot.

Return type:

matplotlib.axes.Axes

Notes

This function extracts opto data from the log, plots the intervals using _plot_laser_intervals, and adds text annotations for each interval. It handles both milliwatt and voltage amplitudes.

cibrrig.plot._create_ax(dims, projection=None)

Create a new figure and axis.

Parameters:

• dims (list) – Dimensions to plot.

• projection (str, optional) – Type of projection for 3D plots.

Returns:

Figure and Axes objects.

Return type:

tuple

cibrrig.plot._setup_colorbar(ax, p, vmin, vmax, colorbar_title)

Set up a colorbar for the plot.

Parameters:

• ax (Axes) – The axes object to add the colorbar to.

• p – The plot object to create the colorbar from.

• vmin (float) – Minimum value for the colorbar.

• vmax (float) – Maximum value for the colorbar.

• colorbar_title (str) – Title for the colorbar.

cibrrig.plot.plot_projection_line_multicondition(X, tbins, intervals, colors, dims=[0, 1], ax=None, alpha=0.5, lw=1, **kwargs)

Plot low-D projection with unique coloring for the given intervals.

Parameters:

• X (array) – Data to plot.

• tbins (array) – Time bins.

• intervals (array) – Start and end times for each condition.

• colors (list) – Colors for each condition.

• dims (list) – Dimensions to plot.

• ax (Axes, optional) – Axes to plot on.

• alpha (float) – Alpha value for transparency.

• lw (float) – Line width.

Returns:

The axes object containing the plot.

Return type:

Axes

cibrrig.plot.plot_projection_line(X, cvar=None, dims=[0, 1], cmap='viridis', **kwargs)

Plot low-d projection as a line. Optionally

Parameters:

• X (array) – Data to plot.

• cvar (array, optional) – Color variable.

• dims (list) – Dimensions to plot.

• cmap (str) – Colormap to use.

• **kwargs – Additional keyword arguments.

Keyword Arguments:

• ax (matplotlib.axes.Axes, optional) – The axes to plot on. If not provided, a new figure and axes will be created.

• color (str, optional) – Color of the line if cvar is not provided. Default is “k” (black).

• alpha (float, optional) – The alpha blending value, between 0 (transparent) and 1 (opaque). Default is 0.5.

• lw (float, optional) – The line width. Default is 0.5.

• vmin (float, optional) – Minimum of the colormap range. If not provided, it’s inferred from cvar.

• vmax (float, optional) – Maximum of the colormap range. If not provided, it’s inferred from cvar.

• colorbar_title (str, optional) – Title for the colorbar. Default is an empty string.

• title (str, optional) – Title for the plot. Only used in 3D plots. Default is an empty string.

• lims (list, optional) – The x, y, (and z for 3D) limits of the plot as [min, max]. Only used in 3D plots. Default is [-4, 4].

• pane_color (color, optional) – Color of the panes in 3D plots. If None, default matplotlib style is used.

• plot_colorbar (bool, optional) – Whether to plot the colorbar. Only used in 3D plots. Default is True.

Returns:

The axes object containing the plot.

Return type:

Axes

cibrrig.plot._plot_projection_line_2D(X, cvar=None, dims=[0, 1], cmap='viridis', color='k', ax=None, alpha=0.5, vmin=None, vmax=None, lw=0.5, colorbar_title='', plot_colorbar=True, **kwargs)

Plot 2D projection line.

Parameters:

• X (array) – Data to plot.

• cvar (array, optional) – Color variable.

• dims (list) – Dimensions to plot.

• cmap (str) – Colormap to use.

• color (str) – Color for the line if cvar is None.

• ax (Axes, optional) – Axes to plot on.

• alpha (float) – Alpha value for transparency.

• vmin (float, optional) – Minimum value for colormap.

• vmax (float, optional) – Maximum value for colormap.

• lw (float) – Line width.

• colorbar_title (str) – Title for the colorbar.

• **kwargs – Additional keyword arguments.

Returns:

The axes object containing the plot.

Return type:

Axes

cibrrig.plot._plot_projection_line_3D(X, cvar=None, dims=[0, 1, 2], cmap='viridis', color='k', ax=None, title='', alpha=0.5, lims=None, pane_color=None, colorbar_title='', plot_colorbar=True, vmin=None, vmax=None, lw=0.5, **kwargs)

Plot 3D projection line.

Parameters:

• X (array) – Data to plot.

• cvar (array, optional) – Color variable.

• dims (list) – Dimensions to plot.

• cmap (str) – Colormap to use.

• color (str) – Color for the line if cvar is None.

• ax (Axes3D, optional) – 3D axes to plot on.

• title (str) – Title for the plot.

• alpha (float) – Alpha value for transparency.

• lims (list) – Limits for the axes.

• pane_color – Color for the panes.

• colorbar_title (str) – Title for the colorbar.

• plot_colorbar (bool) – Whether to plot the colorbar.

• vmin (float, optional) – Minimum value for colormap.

• vmax (float, optional) – Maximum value for colormap.

• lw (float) – Line width.

• **kwargs – Additional keyword arguments.

Returns:

The 3D axes object containing the plot.

Return type:

Axes3D

cibrrig.plot.plot_projection(X, dims, **kwargs)

Plot projection in 2D or 3D.

Parameters:

• X (array) – Data to plot.

• dims (list) – Dimensions to plot.

• **kwargs – Additional keyword arguments.

Keyword Arguments:

• ax (matplotlib.axes.Axes, optional) – The axes to plot on. If not provided, a new figure and axes will be created.

• color (str, optional) – The color of the data points or lines. Default is “k” (black) if no color variable (cvar) is provided.

• alpha (float, optional) – Transparency level for the points. Should be between 0 (fully transparent) and 1 (fully opaque). - Default is 0.5.

• lw (float, optional) – Line width for plotting. Applies if plotting a line plot. Default is 0.5.

• vmin (float, optional) – Minimum value for the colormap if a color variable (cvar) is used. If not specified, it’s inferred from cvar.

• vmax (float, optional) – Maximum value for the colormap if a color variable (cvar) is used. If not specified, it’s inferred from cvar.

• colorbar_title (str, optional) – Title for the colorbar. Default is an empty string.

• title (str, optional) – Title for the plot. Only used in 3D plots. Default is an empty string.

• lims (list, optional) – Axis limits for the plot. Should be a list of [min, max] values. - Default is [-4, 4] for 3D plots.

• pane_color (str, optional) – Background color of the 3D panes in 3D plots. If None, default style is used.

• plot_colorbar (bool, optional) – Whether to include a colorbar in the plot. Only applies to 3D plots when cvar is used. Default is True.

• s (float, optional) – Size of the markers used in the scatter plot. Default is 1.

• cmap (str, optional) – Colormap to use when plotting with a color variable (cvar). Default is “viridis”.

• cvar (array-like, optional) – An array of values used to color the data points. If provided, cmap is applied.

• s – Size of the markers in the scatter plot. Default is 1.

Returns:

Figure and Axes objects.

Return type:

tuple

cibrrig.plot.plot_3D_projection(X, dims=[0, 1, 2], cvar=None, ax=None, title='', s=1, vmin=None, vmax=None, cmap='viridis', c='k', alpha=0.2, lims=None, plot_colorbar=True, colorbar_title='', pane_color=None, **kwargs)

Plot 3D projection.

Parameters:

• X (array) – Data to plot.

• dims (list) – Dimensions to plot.

• cvar (array, optional) – Color variable.

• ax (Axes3D, optional) – 3D axes to plot on.

• title (str) – Title for the plot.

• s (float) – Size of the markers.

• vmin (float, optional) – Minimum value for colormap.

• vmax (float, optional) – Maximum value for colormap.

• cmap (str) – Colormap to use.

• c (str) – Color for the markers if cvar is None.

• alpha (float) – Alpha value for transparency.

• lims (list) – Limits for the axes.

• plot_colorbar (bool) – Whether to plot the colorbar.

• colorbar_title (str) – Title for the colorbar.

• pane_color – Color for the panes.

• **kwargs – Additional keyword arguments.

Returns:

Figure and Axes3D objects.

Return type:

tuple

cibrrig.plot.plot_2D_projection(X, dims=[0, 1], cvar=None, ax=None, title='', s=1, vmin=None, vmax=None, cmap='viridis', c='C1', alpha=0.2, lims=[-4, 4], plot_colorbar=True, colorbar_title='')

Plot 2D projection.

Parameters:

• X (array) – Data to plot.

• dims (list) – Dimensions to plot.

• cvar (array, optional) – Color variable.

• ax (Axes, optional) – Axes to plot on.

• title (str) – Title for the plot.

• s (float) – Size of the markers.

• vmin (float, optional) – Minimum value for colormap.

• vmax (float, optional) – Maximum value for colormap.

• cmap (str) – Colormap to use.

• c (str) – Color for the markers if cvar is None.

• alpha (float) – Alpha value for transparency.

• lims (list) – Limits for the axes.

• plot_colorbar (bool) – Whether to plot the colorbar.

• colorbar_title (str) – Title for the colorbar.

Returns:

Figure and Axes objects.

Return type:

tuple

cibrrig.plot.plot_polar_average(x, y, t, ax=None, t0=None, tf=None, color='k', bins=50, multi='sem', alpha=0.3, **plot_kwargs)

Plot covariate y as a function of phase x on a polar.

If t0,tf are arrays, will average over multiple intervals

Parameters:

• x (1D numpy array) – Phase data with values in the range [-pi, pi].

• y (1D numpy array) – Signal data to be plotted against x.

• t (1D numpy array) – Time data corresponding to x and y.

• ax (matplotlib.axes.Axes, optional) – The axes object to plot on. If None, a new figure and axes are created. Defaults to None.

• t0 (int, float, or list, optional) – Start time(s) for epoch selection. If a list or array, averages over multiple epochs are computed. Defaults to None.

• tf (int, float, or list, optional) – End time(s) for epoch selection, matching the format of t0. Defaults to None.

• color (str or list, optional) – Line color(s) for the plot. Defaults to ‘k’.

• bins (int, optional) – Number of bins for the polar histogram. Defaults to 50.

• multi (str, optional) – Specifies the method for calculating the shaded region. Options are ‘std’ for standard deviation or ‘sem’ for standard error of the mean. Defaults to ‘sem’.

• alpha (float, optional) – Transparency of the shaded region. Defaults to 0.3.

• **plot_kwargs – Additional keyword arguments passed to ax.plot.

Returns:

A tuple containing:

• f: The created figure object (or None if ax was provided).

• ax: The axes object used for plotting.

• y_polar_out: 2D numpy array of the polar data averaged over epochs.

• phase_bins: Phase bin centers for the plot.

Return type:

tuple

Example

>>> plot_polar_average(x, y, t, t0=0, tf=10, color='b', bins=30, multi='std')

cibrrig.plot.plot_reset_curve(breaths, events, wavelength=473, annotate=False, norm=True, plot_tgl=True, n_control=100)

Plot a reset curve for optogenetic stimulation, showing phase-dependent effects on breathing cycles.

Parameters:

• breaths (AlfBunch) – Breath timing data with attributes: ‘times’, ‘IBI’, and ‘duration_sec’.

• events (np.ndarray) – 1D array of stimulation/event times.

• wavelength (int, optional) – Wavelength of optogenetic stimulus. Defaults to 473.

• annotate (bool, optional) – If True, add annotations and color overlays to the plot. Defaults to False.

• norm (bool, optional) – If True, normalizes time to phase (0-1) for plotting. Defaults to True.

• plot_tgl (bool, optional) – If True, creates a plot; if False, returns computed data. Defaults to True.

• n_control (int, optional) – Number of random control points for a control distribution. Defaults to 100.

Returns:

• cycle_stim_time: Normalized/raw times of stimulation relative to breath onset.

• cycle_duration: Normalized/raw breath cycle durations following stimulation.

• cycle_stim_time_rand: Control times for stimulation from random event times.

• cycle_duration_rand: Control breath cycle durations for random events.

Return type:

tuple

cibrrig.plot.plot_sweeps(xt, x, times, pre, post, ax=None, **kwargs)

Time-aligns a trace x to event times specified in times.

Parameters:

• xt (array-like) – Time values corresponding to the signal trace x.

• x (array-like) – Signal trace data to be plotted.

• times (array-like) – Event times to align the trace x to.

• pre (float) – Time before each event to start the trace.

• post (float) – Time after each event to end the trace.

• ax (matplotlib.axes.Axes, optional) – Axes to plot on. If None, a new figure and axes will be created. Default is None.

• **kwargs – Additional keyword arguments passed to ax.plot, such as line style or color.

Returns:

matplotlib axis

Return type:

ax

cibrrig.plot.plot_most_likely_dynamics(model, xlim=(-4, 4), ylim=(-3, 3), nxpts=20, nypts=20, alpha=0.8, ax=None, figsize=(3, 3), colors=[f'C{x}' for x in range(7)], zval=None)

Plotting of underlying vector fields from Linderman Lab

cibrrig.plot.plot_most_likely_dynamics_3D(model, xlim=(-4, 4), ylim=(-3, 3), zlim=(-3, 3), nxpts=10, nypts=10, nzpts=10, alpha=0.2, ax=None, figsize=(3, 3), length=0.2, colors=[f'C{x}' for x in range(7)])

Extension of the linderman vectorfield plot to 3D

cibrrig.plot._clean_3d_axes(ax, title, dims, pane_color, lims=None)

Modify 3D axes to be cleaner:

Set title set axis labels make limits equal turn off grid set background color

Parameters:

• ax (matplotlib.axes._subplots.Axes3DSubplot) – The 3D axes object to customize.

• title (str) – The title of the plot.

• dims (tuple or list of ints) – Dimensions to label the axes, corresponding to the 3D data dimensions (e.g., (0, 1, 2) for first three components).

• pane_color (tuple or None) – RGB color to set for the panes (background of each axis). Use None for default color.

• lims (tuple or list of floats,optional) – If None, autoscales axes. Axis limits to set for x, y, and z axes (e.g., (-1, 1) to set limits for all axes).

Returns:

The modified axes object.

Return type:

ax (matplotlib.axes._subplots.Axes3DSubplot)

Example

ax = fig.add_subplot(111, projection=’3d’) _clean_3d_axes(ax, “3D Plot”, (0, 1, 2), (0.9, 0.9, 0.9, 0.5), (-1, 1))

cibrrig.plot.clean_polar_axis(ax)

Clean the appearance of a polar plot. Use pi/2 (90 degrees) angular ticks, no internal radial ticks, and set labels to mathtext pi

Parameters:

ax (matplotlib.projections.polar.PolarAxes) – The polar axes object to modify.

Example

ax = plt.subplot(projection=’polar’) clean_polar_axis(ax)

cibrrig.plot.clean_linear_radial_axis(ax)

Clean the appearance of a plot with a range o [-pi,pi] but on a normal, linear axis Sets ticks to every pi/2 interval and uses math text.

Parameters:

ax (matplotlib.axes._subplots.AxesSubplot) – The axes object to modify.

Example

ax = plt.subplot() clean_linear_radial_axis(ax)

cibrrig.plot.plot_driftmap_with_trace(spike_times, spike_depths, trace, trace_times, trace_label='', t0=None, tf=None, depth_lim=(None, None), trace_ylim=(None, None), t_bin=0.01, driftmap_kwargs={}, trace_kwargs={}, figsize=(2, 8), use_scalebar=True, use_colorbar=True, cmap=None, raster_ylabel=None)

#TODO: Update documentation #TODO: UPdate to work more intuitively with clusters

Works well as a driftmap, but lass good as a rastermap

Plot a drift map with an covariate trace above.

Built off of ibllib.brainbox.plot.driftmap. This function plots a drift map of spike times and depths, with an overlaid trace such as diaphragm or another continuous signal.

Parameters:

• spike_times (array-like) – Array of spike times.

• spike_depths (array-like) – Array of spike depths corresponding to each spike time.

• trace (array-like) – Continuous signal to overlay on the drift map. Can be multiple columns as long as each row is a timepoint

• trace_times (array-like) – Time points corresponding to the trace signal.

• trace_label (str, optional) – Label for the trace. Defaults to ‘’.

• t0 (float, optional) – Start time for the plot. Defaults to None, which uses the minimum spike time.

• tf (float, optional) – End time for the plot. Defaults to None, which uses the maximum spike time.

• depth_lim (tuple, optional) – Depth limits for the plot. Defaults to (None, None), which uses the min and max spike depths.

• trace_ylim (tuple, optional) – Y-axis limits for the trace plot. Defaults to (None, None), which uses the min and max trace values.

• driftmap_kwargs (dict, optional) – Additional keyword arguments for the drift map plot. Defaults to {}.

• trace_kwargs (dict, optional) – Additional keyword arguments for the trace plot. Defaults to {}.

• figsize (tuple, optional) – Figure size for the plot. Defaults to (2, 8).

• use_scalebar (bool, optional) – Whether to use a scale bar in the plot. Defaults to True.

Returns:

The axes object containing the drift map. matplotlib.axes._subplots.AxesSubplot: The axes object containing the trace plot.

Return type:

matplotlib.axes._subplots.AxesSubplot

cibrrig.plot.replace_timeaxis_with_scalebar(ax, pad=0.025, lw=None, color=None, size=None)

Replace the x-axis with a horizontal bar showing the time scale of the plot.

Parameters:

• ax (matplotlib.axes._subplots.AxesSubplot) – The axes object to modify.

• inverted_y (bool, optional) – Set true if the plot has 0 at the top

• pad (float, optional) – Padding between the scale bar and the plot. Defaults to 0.01.

• lw (float, optional) – Line width for the scale bar. Defaults to None, which uses the default line width.

• color (str, optional) – Color for the scale bar. Defaults to None, which uses the default text color.

• size (float, optional) – Font size for the scale bar. Defaults to None, which uses the default tick size.

cibrrig.plot.trim_yscale_to_lims(ax, ymin, ymax)

cibrrig.plot.plot_peth_and_raster(spike_times, starts, stops=None, pre_time=0.2, post_time=0.2, bin_size=0.01, smoothing=0, error_bars='sem', pethline_kwargs={}, errbar_kwargs={'alpha': 0.5}, eventline_kwargs={'color': plt.rcParams['text.color'], 'ls': '--'}, raster_kwargs={'s': 2, 'marker': '|'}, raster_ylabel='', figsize=(3, 6), subplot_ratio=(1, 5))

Plot a peri-event time histogram and raster plot

Parameters:

• spike_times (array) – spike times

• starts (array) – event times

• stops (array, optional) – stop times. Defaults to None.

• pre_time (float, optional) – time before event to plot. Defaults to 0.2.

• post_time (float, optional) – time after event to plot. Defaults to 0.2.

• bin_size (float, optional) – bin size for histogram. Defaults to 0.01.

• smoothing (float, optional) – smoothing factor for histogram. Defaults to 0.

• error_bars (str, optional) – error bars to plot. Defaults to “sem”.

• pethline_kwargs (dict, optional) – kwargs for the peth line. Defaults to {}.

• errbar_kwargs (dict, optional) – kwargs for the error bars. Defaults to {“alpha”: 0.5}.

• eventline_kwargs (dict, optional) – kwargs for the event line. Defaults to {“color”: plt.rcParams[“text.color”], “ls”: “–“}.

• raster_kwargs (dict, optional) – kwargs for the raster plot. Defaults to {‘s’:2,’marker’:’|’}.

• raster_ylabel (str, optional) – ylabel for the raster plot. Defaults to “”.

• figsize (tuple, optional) – figure size. Defaults to (3, 6).

• subplot_ratio (tuple, optional) – ratio of the subplots. Defaults to (1, 5).

Returns:

matplotlib axis for the raster and peth plots

Return type:

ax_raster, ax_peth