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Compare two neurons from the BANC connectome dataset

Source: R/ggplot2.R
banc_neuron_comparison_plot.Rd

This function creates a visual comparison of two neurons from the BANC (Bilateral Antennal lobe Neuron Connectome) dataset. It generates four different anatomical views to facilitate comparison.

Usage

banc_neuron_comparison_plot(
  neuron1 = NULL,
  neuron2 = NULL,
  neuron3 = NULL,
  neuron1.info = NULL,
  neuron2.info = NULL,
  neuron3.info = NULL,
  volume = NULL,
  region = c("both", "brain", "vnc"),
  banc_brain_neuropil = NULL,
  banc_vnc_neuropil = NULL,
  banc_neuropil = NULL,
  alpha = 0.5,
  filename = NULL,
  width = 16,
  height = 16
)

Arguments

neuron1

A neuronlist object representing the first neuron to be compared.

neuron2

A neuronlist object representing the second neuron to be compared.

neuron3

A neuronlist object representing the third neuron to be compared.

neuron1.info

Character, a vector to be printed on the outputted ggplot in reference to neuron1.

neuron2.info

Character, a vector to be printed on the outputted ggplot in reference to neuron2.

neuron3.info

Character, a vector to be printed on the outputted ggplot in reference to neuron3.

volume

A mesh3d or hxsurf object in BANC space that you wish you co-plot.

region

Character, whether to plot the brain area, VNC area or both (default).

banc_brain_neuropil

A mesh object representing the brain neuropil. Default is banc_brain_neuropil.surf.

banc_vnc_neuropil

A mesh object representing the ventral nerve cord (VNC) neuropil. Default is banc_vnc_neuropil.surf.

banc_neuropil

A mesh object representing the entire neuropil. Default is banc_neuropil.surf.

alpha

Vector of alpha values for neurons 1, 2 and 3. If a single value, applied to all.

filename

Optional. If provided, the plot will be saved to this file. If NULL (default), the plot will be displayed but not saved.

width

Numeric. The width of the output plot in inches. Default is 16.

height

Numeric. The height of the output plot in inches. Default is 16.

Value

If filename is NULL, the function returns a ggplot object. If filename is provided, the function saves the plot and returns invisibly.

Details

The function generates four views of the neurons:

  1. Main view

  2. Side view

  3. Front view (brain only)

  4. VNC (Ventral Nerve Cord) view

Each view applies appropriate rotations and uses different neuropil meshes as backgrounds. The two neurons are plotted in different colors (navy/turquoise for neuron1, red/darkred for neuron2) for easy comparison.

Examples

if (FALSE) { # \dontrun{
# Assuming neuron1 and neuron2 are valid neuron objects
banc.meta <- banctable_query()

# Get some neurons to plot
banc.meta.dnao1 <- subset(banc.meta, cell_type=="DNa01")
dna01 <- banc_read_neuron_meshes(unique(banc.meta.dnao1$root_id))
banc.meta.dnao2 <- subset(banc.meta, cell_type=="DNa02")
dna02 <- banc_read_neuron_meshes(unique(banc.meta.dnao2$root_id))

# Simplify neurons to make them easier to plot
dna01 <- nat::nlapply(dna01,Rvcg::vcgQEdecim,percent = 0.1)
dna02 <- nat::nlapply(dna02,Rvcg::vcgQEdecim,percent = 0.1)

# Make plot!
banc_neuron_comparison_plot(dna01, dna02, neuron1.info = "DNa01",
neuron2.info = "DNa02", filename = "neuron_comparison.png")
} # }