This function creates a complete ggplot2 visualisation for neuron objects, including 'neuron', 'neuronlist', 'mesh3d', and 'hxsurf' objects. It sets up a minimal theme and applies consistent styling to the plot.
Arguments
- x
A 'neuron', 'neuronlist', 'mesh3d', or 'hxsurf' object to be visualised.
- 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
Colour for the lowest Z values. Default is "turquoise".
- cols2
Colour for the highest Z values. Default is "navy".
- alpha
Transparency of the neuron visualisation. Default is 0.5.
- title.col
Colour of the plot title. Default is "darkgrey".
- ...
Additional arguments passed to geom_neuron().
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 visualisation itself.
References
Jefferis, G. S. X. E., Potter, C. J., Chan, A. M., Marin, E. C., Rohlfing, T., Maurer, C. R., & Luo, L. (2007). Comprehensive maps of Drosophila higher olfactory centers: Spatially segregated fruit and pheromone representation. Cell, 128(6), 1187-1203. doi:10.1016/j.cell.2007.01.040
Schneider-Mizell, C. M., Gerhard, S., Longair, M., Kazimiers, T., Li, F., Zwart, M. F., Champion, A., Midgley, F. M., Fetter, R. D., Saalfeld, S., & Cardona, A. (2016). Quantitative neuroanatomy for connectomics in Drosophila. eLife, 5, e12059. doi:10.7554/eLife.12059
See also
geom_neuron
for the underlying geom used in this function.
Examples
if (FALSE) { # \dontrun{
library(nat.ggplot)
# Visualise neurons with brain volume as context
ggneuron(banc.skels,
volume = banc.brain_neuropil,
rotation_matrix = banc_view)
# Visualise the brain neuropil alone
ggneuron(banc.brain_neuropil,
rotation_matrix = banc_view,
cols1 = c("lightblue", "darkblue"))
# Visualise split neurons with custom colours
ggneuron(banc.neurons.flow,
volume = banc.brain_neuropil,
rotation_matrix = banc_view,
info = "LHPD2a1 neurons with axon/dendrite split")
# Visualise neuron meshes
ggneuron(banc.meshes[[1]],
rotation_matrix = banc_view,
cols1 = c("purple", "magenta"),
alpha = 0.8)
} # }