Plotting ToolsΒΆ
The scaffold package provides tools to plot network topology (either point and detailed
networks) and morphologies in the bsb.plotting
module.
To plot a network saved in a bsb instance, you can use:
plot_network_cache(scaffold)
: to plot the network saved in the memory cache after having compiled itplot_network(scaffold)
: to plot a network, adding the keyword argumentfrom_memory=False
if you want to plot a network saved in a previously compiled HDF5 file. The default value isfrom_memory=True
, which plots the version saved in your cache (you should have compiled the network in the current session).plot_network_detailed(scaffold)
: Plots cells represented by their fully detailed morphologies. These plots are usually not able to render more than a 30-50 cells at the same time depending on the complexity of their morphology.
You can also plot morphologies:
plot_morphology(m)
: Plots aMorphology
plot_fiber_morphology(fm)
: Plots aFiberMorphology
plot_voxel_cloud(m.cloud)
: Plots aVoxelCloud
All of the above functions take a fig
keyword argument of type
plotly.graph_objects.Figure
in case you want to modify the figure, or combine
multiple plotting functions on the same figure, such as plotting a morphology and the
voxel cloud of its axon.