read.neuron.swc: Read a neuron in swc file format

In natverse/nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Read a neuron in swc file format

Description

read.neuron.swc reads an SWC file on disk into a fully parsed neuron representation. However we normally recommend using read.neuron(s) since those functions cope with any file type.

read.ngraph.swc reads an SWC file on disk into the more generic (and forgiving) ngraph representation which provides a bridge to the igraph library.

Usage

read.neuron.swc(f, ...)

read.ngraph.swc(f, weights = FALSE, directed = TRUE, ...)

Arguments

f	path to file
...	Additional arguments. read.neuron.swc passes these to as.neuron and then on to neuron. read.neuron.swc passes them to ngraph.
weights	Logical value indicating whether edge weights defined by the 3D distance between points should be added to graph (default FALSE) or a numeric vector of weights.
directed	Whether the resultant graph should be directed (default TRUE)

Details

These functions will accept SWC neurons with multiple trees and arbitrary point index order. However only read.ngraph.swc will accept SWC files with cycles.

These functions would normally be called from read.neuron(s) rather than used directly. The only benefit of using read.neuron.swc is to avoid a very small overhead in identifying the SWC file type. Note that only read.neurons can read many files in one command to construct a neuronlist object.

SWC Format

According to http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC file format has a radius not a diameter specification

See Also

is.swc, read.neuron

natverse/nat documentation built on Feb. 19, 2024, 7:19 a.m.