PYNML-PLOTMORPH(1)

NAME
pynml-plotmorph - manual page for pynml-plotmorph v1.3.21

DESCRIPTION
usage: pynml-plotmorph [-h] [-v] [-nogui] [-plane2d <plane, e.g. xy, yz, zx>]

[-pointFraction <fraction of each population to plot as point cells>]
    [-plotType <type: detailed, constant, schematic, or point>] [-showAxes <axes placement: origin, bottom left>] [-theme <theme: light, dark>] [-upright] [-minWidth <min width of lines>] [-interactive3d] [-saveToFile <Image file name>] [-saveMeshTo <Mesh file name (must end in '.obj' or '.gz')>] [-square] <NeuroML 2 file/SWC cell file>

A script which can generate plots of morphologies in NeuroML 2. It can generate plots of single cells (either detailed or point cells), and networks that include these cells. It can also visualise single cell morphologies from SWC files, although it will first convert these to NeuroML.

  positional arguments:

<NeuroML 2 file/SWC cell file>
    Name of the NeuroML 2 file/SWC cell file

  options:

-h, --help
    show this help message and exit

-v  Verbose output

-nogui
    Don't open plot window

-plane2d <plane, e.g. xy, yz, zx>
    Plane to plot on for 2D plot

-pointFraction <fraction of each population to plot as point cells>
    Fraction of network to plot as point cells

-plotType <type: detailed, constant, schematic, or point>
    Level of detail to plot in

-showAxes <axes placement: origin, bottom left>
    Whether to show reference X, Y, Z axes

-theme <theme: light, dark>
    Theme to use for interactive 3d plotting (not used for 2d plotting)

-upright
    Transform single cell to show it 'upright' in 3D viewer

-minWidth <min width of lines>
    Minimum width of lines to use

-interactive3d
    Show interactive 3D plot

-saveToFile <Image file name>
    Name of the image file, for 2D plot

-saveMeshTo <Mesh file name (must end in '.obj' or '.gz')>
    Name of the file to save 3D mesh data to

-square
    Scale axes so that image is approximately square, for 2D plot

SEE-ALSO
pynml(1), pynml-archive(1), pynml-channelanalysis(1), pynml-channelml2nml(1), pynml-modchananalysis(1), pynml-plotchan(1), pynml-plotmorph(1), pynml-plotspikes(1), pynml-plottimeseries(1), pynml-povray(1), pynml-sonata(1), pynml-summary(1), pynml-swc2nml(1), pynml-tune(1), pynml-xpp(1),

Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.

ENVIRONMENT

pyNeuroML v1.3.21 (libNeuroML v0.6.7, jNeuroML v0.14.0)