plot3d_split: Plot neurons split up by flow centrality

In natverse/hemibrainr: Code for Working with Data from Janelia FlyEM's Hemibrain Project and the flywire data sets``

Plot neurons split up by flow centrality

Description

Plot neurons split up by flow centrality

Usage

plot3d_split(
  someneuronlist,
  prepost = c("BOTH", "PRE", "POST"),
  col = c("#1BB6AF", "#EF7C12", "#C70E7B", "#8FDA04", "#4D4D4D", "#FC6882"),
  splitnode = FALSE,
  WithConnectors = TRUE,
  WithNodes = F,
  soma = NULL,
  soma.alpha = 1,
  transmitters = FALSE,
  transmitter.alpha = 0.3,
  highflow = FALSE,
  lwd = 1,
  radius = NULL,
  already_selected = NULL,
  check.template = FALSE,
  ...
)

nlscan_split(
  someneuronlist,
  already_selected = NULL,
  prepost = c("BOTH", "PRE", "POST"),
  col = c("#1BB6AF", "#EF7C12", "#C70E7B", "#8FDA04", "#4D4D4D", "#FC6882"),
  splitnode = FALSE,
  WithConnectors = TRUE,
  WithNodes = F,
  soma = NULL,
  soma.alpha = 1,
  transmitters = FALSE,
  transmitter.alpha = 0.3,
  highflow = FALSE,
  lwd = 1,
  radius = NULL,
  check.template = FALSE,
  Verbose = TRUE,
  Wait = TRUE,
  sleep = 0.1,
  selected_file = NULL,
  selected_col = "#fadadd",
  yaml = TRUE,
  brain = FALSE,
  ...
)

plot3d_somas(
  someneuronlist,
  col = hemibrain_bright_colors["green"],
  radius = 300,
  soma.alpha = 1,
  volume = NULL,
  invert = FALSE
)

Arguments

someneuronlist	a neuronlist or neuron object that has been modified by flow.centrality.
prepost	whether to plot input (POST-) or output (PRE-) synapses, or both (default).
col	colours of sections. Defaults to orange or axons, green for primary dendrite, blue for dendrites and pink for nodes with no flow.
splitnode	if TRUE, a magenta sphere is placed at the location of the axon-dendrite split. Possible a putative action potential initiation site?
WithConnectors	whether to plot the anatomical location of pre (red) and post (cyan) synapses.
WithNodes	whether to plot branch points.
soma	whether to plot a soma, and what the radius should be. If NULL, an appropriate value is guessed.
soma.alpha	numeric, alpha transparency value for plotting the soma. Passed to rgl::spheres3d
transmitters	logical. If TRUE, and transmitter identities are given in each neuron's meta data at neuron$connectors, then synapses. are plotted in their transmitter colours. Transmitter identity is given by the colour of a halo around each synapse. The colours correspond to entries in paper_colours.
transmitter.alpha	numeric, alpha transparency value for a coloured halo indicative of transmitter identity around synapses. Passed to rgl::spheres3d.
highflow	whether to plot the nodes of highest (with in one standard deviation less than maximum) flow centrality (pink points).
lwd	Line width (default 1).
radius	For connectors and axon-dendrite split node (default 1). If NULL, an appropriate value is guessed.
already_selected	a vector of IDs for neurons that are already considered selected. If NULL then no neurons are considered selected to start with.
check.template	check which template space someneuronlist is in, in order to set default plotting settings.
...	additional arguments passed to methods.
Verbose	logical indicating that info about each selected neuron should be printed (default TRUE)
Wait	logical indicating that there should be a pause between each displayed neuron
sleep	time to pause between each displayed neuron when Wait=TRUE
selected_file	an optional path to a yaml file that already contains a selection
selected_col	the color in which selected neurons (such as those specified in selected_file) should be plotted
yaml	a logical indicating that selections should be saved to disk in (human-readable) yaml rather than (machine-readable) rda format
brain	a template brain to plot. FALSE results in no brain plotted.
volume	a mesh3d or hxsurf object. Only somas outside this volume will be plotted.
invert	logical, if TRUE only somas outside volume will be plotted, if FALSE, only those inside.

Value

Plots coloured neuron(s)

See Also

flow_centrality

natverse/hemibrainr documentation built on July 17, 2025, 4:24 a.m.