netpyne.plotting.plotTimeSeries

Functions:

plotLFPTimeSeries([LFPData, axis, ...])	Function to produce a line plot of LFP electrode signals
plotCSDTimeSeries([CSDData, axis, ...])	"
plotTimeSeries(data[, label, title, yLabel, ...])	Function to produce a line plot of electrode signals (currently, LFP or CSD)

netpyne.plotting.plotTimeSeries.plotLFPTimeSeries(LFPData=None, axis=None, timeRange=None, electrodes=['avg', 'all'], pop=None, separation=1.0, normSignal=False, filtFreq=False, filtOrder=3, detrend=False, orderInverse=True, overlay=False, scalebar=True, legend=True, colorList=None, returnPlotter=False, **kwargs)

Function to produce a line plot of LFP electrode signals

Parameters:

• LFPData (dict, str) –

  The data necessary to plot the LFP signals.

  Default: None uses analysis.prepareLFP to produce LFPData using the current NetPyNE sim object.

  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

• electrodes (list) –

  A list of the electrodes to plot from.

  Default: ['avg', 'all'] plots each electrode as well as their average

• pop (str) –

  A population name to calculate signals from.

  Default: None uses all populations.

• separation (float) –

  Use to increase or decrease distance between signals on the plot.

  Default: 1.0

• normSignal (bool) –

  Whether to normalize the data.

  Default: False

• filtFreq (int or list) –

  Frequency for low-pass filter (int) or frequencies for bandpass filter in a list: [low, high]

  Default: None does not filter the data

• filtOrder (int) –

  Order of the filter defined by filtFreq.

  Default: 3

• detrend (bool) –

  Whether to detrend the data.

  Default: False

• orderInverse (bool) –

  Whether to invert the order of plotting.

  Default: True

• overlay (bool) –

  Option to label signals with a color-matched overlay.

  Default: False

• scalebar (bool) –

  Whether to to add a scalebar to the plot.

  Default: True

• 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

• alpha (float) – line opacity (0-1)

Returns:

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

Return type:

matplotlib figure

netpyne.plotting.plotTimeSeries.plotCSDTimeSeries(CSDData=None, axis=None, timeRange=None, electrodes=['avg', 'all'], pop=None, separation=1.0, orderInverse=True, overlay=False, scalebar=True, legend=True, colorList=None, returnPlotter=False, **kwargs)

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Parameters:

• CSDData (dict, str) –

  The data necessary to plot the CSD signals.

  Default: None uses analysis.prepareCSD to produce CSDData using the current NetPyNE sim object.

  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

• electrodes (list) –

  A list of the electrodes to plot from.

  Default: ['avg', 'all'] plots each electrode as well as their average

• pop (str) –

  A population name to calculate signals from.

  Default: None uses all populations.

• separation (float) –

  Use to increase or decrease distance between signals on the plot.

  Default: 1.0

• orderInverse (bool) –

  Whether to invert the order of plotting.

  Default: True

• overlay (bool) –

  Option to label signals with a color-matched overlay.

  Default: False

• scalebar (bool) –

  Whether to to add a scalebar to the plot.

  Default: True

• 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

• alpha (float) – line opacity (0-1)

Returns:

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

Return type:

matplotlib figure

netpyne.plotting.plotTimeSeries.plotTimeSeries(data, label='TimeSeries', title='Time Series Plot', yLabel=None, axis=None, pop=None, separation=1.0, orderInverse=True, overlay=False, scalebar=True, legend=True, colorList=None, returnPlotter=False, **kwargs)

Function to produce a line plot of electrode signals (currently, LFP or CSD)

Parameters:

• data (dict, str) – The data necessary to plot the signals.

• axis (matplotlib axis) –

  The axis to plot into, allowing overlaying of plots.

  Default: None produces a new figure and axis.

• pop (str) –

  A population name to calculate signals from.

  Default: None uses all populations.

• separation (float) –

  Use to increase or decrease distance between signals on the plot.

  Default: 1.0

• orderInverse (bool) –

  Whether to invert the order of plotting.

  Default: True

• overlay (bool) –

  Option to label signals with a color-matched overlay.

  Default: False

• scalebar (bool) –

  Whether to to add a scalebar to the plot.

  Default: True

• 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

• alpha (float) – line opacity (0-1)

Returns:

time series plot – By default, returns the figure. If returnPlotter is True, instead returns the NetPyNE MetaFig.

Return type:

matplotlib figure