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, legend=True, colorList=None, orderInverse=False, returnPlotter=False, **kwargs)[source]

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

  • 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