netpyne.analysis.network

Module for analyzing and plotting connectivity-related results

Functions:

plotConn([includePre, includePost, feature, ...])

Function for/to <short description of netpyne.analysis.network.plotConn>

plot2Dnet([include, view, showConns, ...])

Function for/to <short description of netpyne.analysis.network.plot2Dnet>

plot2Dfiring([include, view, popColors, ...])

Function for/to <short description of netpyne.analysis.network.plot2Dnet>

calculateDisynaptic([includePost, ...])

Function for/to <short description of netpyne.analysis.network.calculateDisynaptic>

netpyne.analysis.network.plotConn(includePre=['all'], includePost=['all'], feature='strength', orderBy='gid', groupBy='pop', groupByIntervalPre=None, groupByIntervalPost=None, graphType='matrix', removeWeightNorm=False, synOrConn='syn', synMech=None, connsFile=None, tagsFile=None, clim=None, figSize=(8, 8), fontSize=12, saveData=None, saveFig=None, showFig=True, logPlot=False)[source]

Function for/to <short description of netpyne.analysis.network.plotConn>

Parameters
  • includePre (list) – List of presynaptic cells to include. Default: ['all'] Options: ['all'] plots all cells and stimulations, ['allNetStims'] plots just stimulations, ['popName1'] plots a single population, ['popName1', 'popName2'] plots multiple populations, [120] plots a single cell, [120, 130] plots multiple cells, [('popName1', 56)] plots a cell from a specific population, [('popName1', [0, 1]), ('popName2', [4, 5, 6])], plots cells from multiple populations

  • includePost (list) – List of postsynaptic cells to include. Default: ['all'] Options: same as in includePre

  • feature (str) – Feature to show in the connectivity plot. The only features applicable to groupBy='cell' are 'weight', 'delay' and 'numConns'. Default: 'strength' Options: 'weight' weight of connection, 'delay' delay in connection, 'numConns' number of connections, 'probability' probabiluty of connection, 'strength' weight * probability, 'convergence' number of presynaptic cells per postynaptic one, 'divergence' number of postsynaptic cells per presynaptic one

  • orderBy (str) – Unique numeric cell property by which to order x and y axes. Default: 'gid' Options: 'gid', 'y', 'ynorm'

  • groupBy (str) – Plot connectivity for populations, individual cells, or by other numeric tags such as 'y'. Default: 'pop' Options: 'pop', 'cell', 'y'

  • groupByIntervalPre (int or float) – Interval of groupBy feature to group presynaptic cells by in connectivity plot, e.g. 100 to group by cortical depth in steps of 100 um. Default: None Options: <option> <description of option>

  • groupByIntervalPost (int or float) – Interval of groupBy feature to group postsynaptic cells by in connectivity plot, e.g. 100 to group by cortical depth in steps of 100 um. Default: None Options: <option> <description of option>

  • graphType (str) – Type of graph to represent data. Default: 'matrix' Options: 'matrix', 'bar', 'pie'

  • removeWeightNorm (bool) – Default: False Options: <option> <description of option>

  • synOrConn (str) – Use synapses or connections; note one connection can have multiple synapses. Default: 'syn' Options: 'syn', 'conn'

  • synMech (list) – Show results only for these synaptic mechanisms, e.g. ['AMPA', 'GABAA', ...]. Default: None Options: <option> <description of option>

  • connsFile (str) – Path to a saved data file of connectivity to plot from. Default: None Options: <option> <description of option>

  • tagsFile (str) – Path to a saved tags file to use in connectivity plot. Default: None Options: <option> <description of option>

  • clim (list [min, max]) – List of numeric values for the limits of the colorbar. Default: None uses the min and max of the connectivity matrix Options: <option> <description of option>

  • figSize (list [width, height]) – Size of figure in inches. Default: (8, 8) Options: <option> <description of option>

  • fontSize (int) – Font size on figure. Default: 12 Options: <option> <description of option>

  • saveData (bool or str) – Whether and where to save the data used to generate the plot. Default: False Options: True autosaves the data, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.pkl' and '.json'

  • saveFig (bool or str) – Whether and where to save the figure. Default: False Options: True autosaves the figure, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.png', '.jpg', '.eps', and '.tiff'

  • showFig (bool) – Shows the figure if True. Default: True Options: <option> <description of option>

netpyne.analysis.network.plot2Dnet(include=['allCells'], view='xy', showConns=True, popColors=None, tagsFile=None, figSize=(12, 12), fontSize=12, saveData=None, saveFig=None, showFig=True, lineWidth=0.1)[source]

Function for/to <short description of netpyne.analysis.network.plot2Dnet>

Parameters
  • include (list) – List of presynaptic cells to include. Default: ['allCells'] Options: ['all'] plots all cells and stimulations, ['allNetStims'] plots just stimulations, ['popName1'] plots a single population, ['popName1', 'popName2'] plots multiple populations, [120] plots a single cell, [120, 130] plots multiple cells, [('popName1', 56)] plots a cell from a specific population, [('popName1', [0, 1]), ('popName2', [4, 5, 6])], plots cells from multiple populations

  • view (str) – Perspective of view. Default: 'xy' front view, Options: 'xz' top-down view

  • showConns (bool) – Whether to show connections or not. Default: True Options: <option> <description of option>

  • popColors (dict) – Dictionary with custom color (value) used for each population (key). Default: None uses standard colors Options: <option> <description of option>

  • tagsFile (str) – Path to a saved tags file to use in connectivity plot. Default: None Options: <option> <description of option>

  • figSize (list [width, height]) – Size of figure in inches. Default: (12, 12) Options: <option> <description of option>

  • fontSize (int) – Font size on figure. Default: 12 Options: <option> <description of option>

  • saveData (bool or str) – Whether and where to save the data used to generate the plot. Default: False Options: True autosaves the data, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.pkl' and '.json'

  • saveFig (bool or str) – Whether and where to save the figure. Default: False Options: True autosaves the figure, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.png', '.jpg', '.eps', and '.tiff'

  • showFig (bool) –

    Shows the figure if True.

    Default: True Options: <option> <description of option>

    lineWidth: float

    Width of connection lines. Default: 0.1 Options: <option> <description of option>

netpyne.analysis.network.plot2Dfiring(include=['allCells'], view='xy', popColors=None, timeRange=None, spikeBin=5, figSize=(12, 12), fontSize=12, saveData=None, saveFig=None, showFig=True, lineWidth=0.1)[source]

Function for/to <short description of netpyne.analysis.network.plot2Dnet>

Parameters
  • include (list) – List of presynaptic cells to include. Default: ['allCells'] Options: ['all'] plots all cells and stimulations, ['allNetStims'] plots just stimulations, ['popName1'] plots a single population, ['popName1', 'popName2'] plots multiple populations, [120] plots a single cell, [120, 130] plots multiple cells, [('popName1', 56)] plots a cell from a specific population, [('popName1', [0, 1]), ('popName2', [4, 5, 6])], plots cells from multiple populations

  • view (str) – Perspective of view. Default: 'xy' front view, Options: 'xz' top-down view

popColorsdict

Dictionary with custom color (value) used for each population (key). Default: None uses standard colors Options: <option> <description of option>

figSizelist [width, height]

Size of figure in inches. Default: (12, 12) Options: <option> <description of option>

fontSizeint

Font size on figure. Default: 12 Options: <option> <description of option>

saveDatabool or str

Whether and where to save the data used to generate the plot. Default: False Options: True autosaves the data, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.pkl' and '.json'

saveFigbool or str

Whether and where to save the figure. Default: False Options: True autosaves the figure, '/path/filename.ext' saves to a custom path and filename, valid file extensions are '.png', '.jpg', '.eps', and '.tiff'

showFigbool

Shows the figure if True. Default: True Options: <option> <description of option>

lineWidth: float

Width of connection lines. Default: 0.1 Options: <option> <description of option>

netpyne.analysis.network.calculateDisynaptic(includePost=['allCells'], includePre=['allCells'], includePrePre=['allCells'], tags=None, conns=None, tagsFile=None, connsFile=None)[source]

Function for/to <short description of netpyne.analysis.network.calculateDisynaptic>

Parameters
  • includePost (list) – <Short description of includePost> Default: ['allCells'] Options: <option> <description of option>

  • includePre (list) – <Short description of includePre> Default: ['allCells'] Options: <option> <description of option>

  • includePrePre (list) – <Short description of includePrePre> Default: ['allCells'] Options: <option> <description of option>

  • tags (<None?>) – <Short description of tags> Default: None Options: <option> <description of option>

  • conns (<None?>) – <Short description of conns> Default: None Options: <option> <description of option>

  • tagsFile (<None?>) – <Short description of tagsFile> Default: None Options: <option> <description of option>

  • connsFile (<None?>) – <Short description of connsFile> Default: None Options: <option> <description of option>