Create a ggplot2 Visualisation of Neuron Objects

This function creates a complete ggplot2 visualization for neuron objects, including 'neuron', 'neuronlist', 'mesh3d', and 'hxsurf' objects. It sets up a minimal theme and applies consistent styling to the plot.

Usage

ggneuron(
  x,
  volume = NULL,
  info = NULL,
  rotation_matrix = NULL,
  cols1 = c("turquoise", "navy"),
  cols2 = c("grey75", "grey50"),
  alpha = 0.5,
  title.col = "darkgrey",
  ...
)

Arguments

x

A 'neuron', 'neuronlist', 'mesh3d', or 'hxsurf' object to be visualized.

volume

a brain/neuropil volume to be plotted in grey, for context. Defaults to NULL, no volume plotted.

info

Optional. A string to be used as the plot title.

rotation_matrix

An optional 4x4 rotation matrix to apply to the neuron coordinates.

cols1

Color for the lowest Z values. Default is "turquoise".

cols2

Color for the highest Z values. Default is "navy".

alpha

Transparency of the neuron visualization. Default is 0.5.

title.col

Color of the plot title. Default is "darkgrey".

...

Additional arguments passed to geom_neuron().

Value

A ggplot2 object representing the neuron visualization.

Details

This function wraps around geom_neuron() to create a complete plot with a consistent, minimal theme. It removes axes, legends, and other extraneous elements to focus on the neuron visualization itself.

See also

geom_neuron for the underlying geom used in this function.

Examples

if (FALSE) { # \dontrun{
# Visualize the banc volume
ggneuron(banc_neuropil.surf, banc.surf)

# Visualize the banc brain neuropil
ggneuron(banc_neuropil.surf,
rotation_matrix = bancr:::banc_rotation_matrices[["front"]])

# See constituents of a neuronlist
ggneuron(nat::Cell07PNs, volume = nat::MBL.surf,
root = 10, high = "red", low = "black")
} # }