netpyne.plotting.plotSpikeHist module

netpyne.plotting.plotSpikeHist.plotSpikeHist(histData=None, axis=None, timeRange=None, popNumCells=None, popLabels=None, popColors=None, binSize=5, histType='step', stacked=False, cumulative=False, log=False, density=False, legend=True, colorList=None, returnPlotter=False, **kwargs)

Function to produce a histogram plot of cell spiking

NetPyNE Options:

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

  Default: ['allCells', 'eachPop'] includes average of all cells and each population of cells

  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:

• histData (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

• 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.

• binSize (int) –

  Size of bin in ms to use for spike histogram.

  Default: 5

• histType (str) –

  Type of histogram to plot (‘step’, ‘stepfilled’, ‘bar’, ‘barstacked’)

  Default: 'step'

• stacked (bool) –

  Whether to stack populations on top of each other

  Default: False

• cumulative (bool) –

  Whether each bin is cumulative

  Default: False

• log (bool) –

  Whether to use a log axis

  Default: False

• density (bool) –

  Whether to normalize data

  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.

• 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

• linewidth (int) – line width

Returns:

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

Return type:

matplotlib figure