Create ggplot2 Geom Layer for Neuron Visualization

This function creates a ggplot2 geom layer for visualizing neuron objects. It supports 'neuron', 'neuronlist', and 'mesh3d' objects.

Usage

geom_neuron(
  x,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'neuron'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'neuronlist'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'mesh3d'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'hxsurf'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class '`NULL`'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'list'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'matrix'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'data.frame'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'dotprops'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'synapticneuron'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

# S3 method for class 'splitneuron'
geom_neuron(
  x = NULL,
  rotation_matrix = NULL,
  root = 3,
  cols = c("navy", "turquoise"),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

Arguments

x: A 'neuron', 'neuronlist', or 'mesh3d' object to be visualized.
rotation_matrix: An optional 4x4 rotation matrix to apply to the neuron coordinates.
root: Numeric, if >0 and x is or contains neuron objects, then the root node is plotted as a dot of size root. If FALSE or 0 no root node is plotted.
cols: The color to plot the neurons in. If length(cols)==length(x) each neuron will be coloured by its index in x applied to cols.
stat: The statistical transformation to use on the data for this layer.
position: Position adjustment, either as a string, or the result of a call to a position adjustment function.
na.rm: If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend: logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped.
inherit.aes: If FALSE, overrides the default aesthetics, rather than combining with them.
...: Other arguments passed on to layer().

Value

A list of ggplot2 geom layers for visualizing the neuron.

Examples

if (FALSE) { # \dontrun{
library(ggplot2)
ggplot() + geom_neuron(nat::Cell07PNs[[1]], root = 10)
ggplot() + geom_neuron(nat::Cell07PNs)
ggplot() + geom_neuron(nat::MBL.surf)
} # }