Fine-tuning Skeletons#

In this example we will demonstrate various ways to fine-tune plots with skeletons.

By now, you should already have a basic understanding on how to plot neurons in NAVis (2d vs 3d plots, the various backends and plotting methods, etc.) - if not, check out the plotting tutorial.

We will focus on how to finetune plot2d plots because matplotlib is much more flexible than the plot3d backends when it comes to rendering lines. That said: some of the things we show here will also work for the other backends (Octarine, Vispy and K3d) - just not all.

Radii#

If your skeletons have radii (i.e. there is a non-empty radius column in their .nodes SWC table), you can plot them as tubes instead of lines using the radius parameter. By default, radius is set to True but will quietly fall back to False if there is no radius information. Here's an example:

import navis
import matplotlib.pyplot as plt

# Load a neuron
n = navis.example_neurons(1, kind="skeleton")

# Plot as tubes (this is the default)
fig, ax = navis.plot2d(n, view=("x", "-z"), method="2d", radius=True)
plt.tight_layout()

Setting radius=False will plot skeletons as simple lines. This can be useful if you have many neurons because it is faster.

fig, ax = navis.plot2d(n, view=("x", "-z"), method="2d", radius=False)
plt.tight_layout()

Line width#

You can change the line width of the skeletons using the linewidth parameter. The default is 1.

fig, ax = navis.plot2d(
    n,
    view=("x", "-z"),
    method="2d",
    radius=False,
    linewidth=2,  # default linewidth is 1
)

linewidth can also be used to scale the size of the tubes when radius=True:

fig, ax = navis.plot2d(
    n,
    view=("x", "-z"),
    method="2d",
    radius=True,
    linewidth=2,  # double the tube radii
)

Line style#

When radius=False, you can change the line style of the skeletons using the linestyle parameter. The default is "-" (i.e. a solid line).

fig, ax = navis.plot2d(
    n,
    view=("x", "-z"),
    method="2d",
    radius=False,
    linewidth=2,
    linestyle="--"  # dashed line
)

The radius and linewidth parameters will also work with plot3d but the linestyle parameter will not.

Total running time of the script: ( 0 minutes 2.004 seconds)

Download Python source code: plot_04_plotting_skeletons.py

Download Jupyter notebook: plot_04_plotting_skeletons.ipynb

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