Plot neurons split up by flow centrality
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 )
someneuronlist | a neuronlist or neuron object that has been modified by flow.centrality. |
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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 |
soma.alpha | numeric, alpha transparency value for plotting the soma. Passed to |
transmitters | logical. If |
transmitter.alpha | numeric, alpha transparency value for a coloured halo indicative of transmitter identity around synapses. Passed to |
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 |
already_selected | a vector of IDs for neurons that are already considered selected. If |
check.template | check which template space |
... | 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. |
volume | a |
invert | logical, if |
Plots coloured neuron(s)