netpyne.plotting.plotRaster

Functions:

plotRaster([rasterData, axis, timeRange, ...])

Function to produce a raster plot of cell spiking

netpyne.plotting.plotRaster.plotRaster(rasterData=None, axis=None, timeRange=None, maxSpikes=100000000.0, orderBy='gid', popRates=True, popNumCells=None, popLabels=None, popColors=None, syncLines=False, colorbyPhase=None, legend=True, colorList=None, orderInverse=False, returnPlotter=False, **kwargs)

Function to produce a raster plot of cell spiking

NetPyNE Options:

• include (str, int, list) – Cells and/or NetStims to return information from.

  Default: ['allCells'] includes all cells and no NetStims

  Options: (1) 'all' includes all cells and all NetStims, (2) 'allNetStims' includes all NetStims but no cells, (3) a str which matches a popLabel includes all cells in that pop, (4) a str which matches a NetStim name includes that NetStim, (5) an int includes the cell with that global identifier (GID), (6) a list of ints includes the cells with those GIDS, (7) a list with two items, the first of which is a str matching a popLabel and the second of which is an int (or a list of ints), includes the relative cell(s) from that population (e.g. (['popName', [0, 1]]) includes the first two cells in popName.

• sim (NetPyNE sim object) – The sim object from which to get data.

  Default: None uses the current NetPyNE sim object

Parameters:

• rasterData (list, tuple, dict, str) –

  The data necessary to plot the raster (spike times and spike indices, at minimum).

  Default: None uses analysis.prepareRaster to produce rasterData using the current NetPyNE sim object.

  Options: if a list or a tuple, the first item must be a list of spike times and the second item must be a list the same length of spike indices (the id of the cell corresponding to that spike time). Optionally, a third item may be a list of ints representing the number of cells in each population (in lieu of popNumCells). Optionally, a fourth item may be a list of strs representing the population names (in lieu of popLabels).

  If a dict it must have keys 'spkTimes' and 'spkInds' and may optionally include 'popNumCells' and 'popLabels'.

  If a str it must represent a file path to previously saved data.

• axis (matplotlib axis) –

  The axis to plot into, allowing overlaying of plots.

  Default: None produces a new figure and axis.

• timeRange (list) –

  Time range to include in the raster: [min, max].

  Default: None uses the entire simulation

• maxSpikes (int) –

  The maximum number of spikes to include (by reducing the max time range).

  Default: 1e8

• orderBy (str) –

  How to order the cells along the y-axis.

  Default: 'gid' orders cells by their index

  Options: any NetPyNe cell tag, e.g. 'pop', 'x', 'ynorm' .

• popRates (bool) –

  whether to include the spiking rates in the plot title and legend.

  Default: True includes detailed pop information on plot.

  Options: False only includes pop names. 'minimal' includes minimal pop information.

• popNumCells (list) –

  A list of ints representing the number of cells in each population.

  Default: None puts all cells into a single population.

• popLabels (list) –

  A list of strs of population names. Must be the same length as popNumCells.

  Default: None uses generic names.

• popColors (dict) –

  A dict of popLabels and their desired color.

  Default: None draws from the NetPyNE default colorList.

• syncLines (bool) –

  Calculate synchrony measure and plot vertical lines for each spike to evidence synchrony if True.

  Default: False

• colorbyPhase (dict) –

  Dictionary specifying conditions to plot spikes colored by the phase of a simultaneous signal, filtered in a given range

  Default: None colors spikes according to other options (by populations)

  Dictionary entries:

  'signal' specifies the signal. Options are: 'LFP', which takes the signal from the local fiel potential generated in the ongoing simulation, a numpy array of scalars (for example, an external signal used for stimulation), or an external pickle file,

  'fs' is the sampling frequency, which should be specified when the signal is obtained from external sources (pickle file or numpy array). Otherwise, it is assumed to be 1000 Hz. If the signal is specified by 'LFP', then the sampling rate is obtained from the internal simulation (cfg.recordStep),

  'electrode' selects the electrode from the LFP setup. Default is electrode 1,

  'filtFreq' is a list specifying the range for filtering the signal (band-pass). For example, [4,8] to select theta rhythm. The default is a very broadband filtering (essentially, the raw signal) [1,500],

  'filtOrder' is the filter order (Butterworth) to process the signal,

  'pop_background' is a boolean option to color each population alternately with a gray background, for better visualization. The default is False,

  'include_signal' is a boolean option to plot the filtered signal below the raster plot. The default is False.

• legend (bool) –

  Whether or not to add a legend to the plot.

  Default: True adds a legend.

• colorList (list) –

  A list of colors to draw from when plotting.

  Default: None uses the default NetPyNE colorList.

• orderInverse (bool) –

  Whether or not to invert the y axis (useful if populations are defined top-down).

  Default: False does not invert the y-axis.

• returnPlotter (bool) –

  Whether to return the figure or the NetPyNE MetaFig object.

  Default: False returns the figure.

Plot Options:

• showFig (bool) – Whether to show the figure.

  Default: False

• saveFig (bool) – Whether to save the figure.

  Default: False

• overwrite (bool) – whether to overwrite existing figure files.

  Default: True overwrites the figure file

  Options: False adds a number to the file name to prevent overwriting

• legendKwargs (dict) – a dict containing any or all legend kwargs. These include 'title', 'loc', 'fontsize', 'bbox_to_anchor', 'borderaxespad', and 'handlelength'.

• rcParams (dict) – a dict containing any or all matplotlib rcParams. To see all options, execute import matplotlib; print(matplotlib.rcParams) in Python. Any options in this dict will be used for this current figure and then returned to their prior settings.

• title (str) – the axis title

• xlabel (str) – label for x-axis

• ylabel (str) – label for y-axis

• s (int) – marker size

• marker (str) – marker symbol

• linewidth (int) – line width

Returns:

rasterPlot – By default, returns the figure. If returnPlotter is True, instead returns the NetPyNE MetaFig.

Return type:

matplotlib figure