rootpoints: Return the root, branch, or end points of a neuron or graph

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

Return the root, branch, or end points of a neuron or graph

Description

rootpoints returns the root point(s) (one per tree, often the soma).

branchpoints returns the branch points.

endpoints returns the end points (aka leaf nodes); the root point will be returned if it also a leaf node.

Usage

rootpoints(x, ...)

## Default S3 method:
rootpoints(x, ...)

## S3 method for class 'neuron'
rootpoints(x, subtrees = 1, ...)

## S3 method for class 'igraph'
rootpoints(x, ...)

branchpoints(x, ...)

## Default S3 method:
branchpoints(x, ...)

## S3 method for class 'neuron'
branchpoints(x, subtrees = 1, ...)

## S3 method for class 'igraph'
branchpoints(x, ...)

endpoints(x, ...)

## S3 method for class 'neuron'
endpoints(x, subtrees = 1, ...)

## S3 method for class 'igraph'
endpoints(x, ...)

## Default S3 method:
endpoints(x, ...)

Arguments

x	Neuron or other object (e.g. igraph) which might have roots
...	Further arguments passed to methods (for ngraph or igraph objects eventually graph.nodes)).
subtrees	Integer index of the fully connected subtree in x$SubTrees. Only applicable when a neuron consists of multiple unconnected subtrees.

Details

A neuron may have multiple subtrees and therefore multiple roots. At present there is discrepancy between the *.neuron and *.igraph methods. For neurons we return the node indices, for igraph/ngraph objects the node identifiers (aka names/PointNo)

branchpoints.neuron returns a list if more than one subtree is specified

Value

FIXME Raw indices (in range 1:N) of vertices when x is a neuron, integer point identifier (aka PointNo) otherwise.

See Also

graph.nodes, ngraph

Other neuron: neuron(), ngraph(), plot.dotprops(), potential_synapses(), prune(), resample(), spine(), subset.neuron()

Examples

rootpoints(Cell07PNs[[1]])
endpoints(Cell07PNs[[1]])

jefferis/nat documentation built on Feb. 22, 2024, 12:45 p.m.