navis.plot1d¶

navis.plot1d(x, ax=None, color=None, color_by=None, palette=None, **kwargs)[source]¶

Plot neuron topology in 1D according to Cuntz et al. (2010).

This function breaks a neurons into segments between branch points. See Cuntz et al., PLoS Computational Biology (2010) for detailed explanation. For very complex neurons, this neuron “barcode” can get fairly complicated - make sure to zoom in.

Parameters:

x (TreeNeuron | NeuronList) – Neuron(s) to plot.
ax (matplotlib.ax, optional) –
color (tuple | dict) – Color. If dict must map neuron UUID to color.
palette (str | array | list of arrays, default=None) – Name of a matplotlib or seaborn palette. If color is not specified will pick colors from this palette.
color_by (str | array | list of arrays, default = None) – Can be the name of a column in the node table of TreeNeurons or an array of (numerical or categorical) values for each node. Numerical values will be normalized. You can control the normalization by passing a vmin and/or vmax parameter.
**kwargs – Will be passed to matplotlib.patches.Rectangle.

Return type:

matplotlib.ax

Examples

>>> import navis
>>> import matplotlib.pyplot as plt
>>> n = navis.example_neurons(2)
>>> ax = navis.plot1d(n)
>>> plt.show() 

Close figures (only relevant for doctests)

>>> plt.close('all')

See the plotting tutorial for more examples.