prune_vertices: Prune selected vertices or edges from a neuron

Description

prune_vertices removes vertices from a neuron

prune_edges removes edges (and any unreferenced vertices)

Usage

prune_vertices(x, verticestoprune, invert = FALSE, ...)
prune_edges(x, edges, invert = FALSE, ...)

Value

A pruned neuron

Arguments

x: A neuron to prune. This can be any object that can be converted by as.ngraph --- see details.
verticestoprune: An integer vector describing which vertices to remove.
invert: Whether to keep vertices rather than dropping them (default FALSE).
...: Additional arguments passed to as.neuron.ngraph
edges: The edges to remove. One of i) an Nx2 matrix, each row specifying a single edge defined by its raw edge id, ii) an integer vector defining a path of raw vertex ids or iii) an igraph.es edge sequence --- see detaiuls and the P and path arguments of igraph::E.

Details

These are relatively low-level functions and you will probably want to use subset.neuron or prune.neuron and friends in many cases.

Note that prune_vertices and prune_edges both use raw vertex ids to specify the vertices/edges to be removed. If you want to use the id in the PointNo field, then you must translate yourself (see examples).

Both prune_vertices and prune_edges first convert their input x to the ngraph representation of the neuron befor removing points. The input x can therefore be in any form compatible with as.ngraph including an existing ngraph. There is an additional requirement that the input must be compatible with xyzmatrix if invert=TRUE.

Note that the edges argument of prune_edges must specify a path traversing a set of vertices in a valid order. However if the input is a matrix or vector the direction of each individual edge in this path is ignored. So if your neuron has edges 2->1 2->3 3->4 then an edge sequence 1:3 would successfully delete 2 edges.

Examples

Run this code

n=prune_vertices(Cell07PNs[[1]], 1:25)
# original neuron
plot(Cell07PNs[[1]])
# with pruned neuron superimposed
plot(n, col='green', lwd=3, add=TRUE)

# use the PointNo field (= the original id from an SWC file)
n2=prune_vertices(n, match(26:30, n$d$PointNo))
y=prune_edges(Cell07PNs[[1]], edges=1:25)

# remove the spine of a neuron
spine_ids=spine(Cell07PNs[[1]], rval='ids')
pruned=prune_edges(Cell07PNs[[1]], spine_ids)

# NB this is subtly different from this, which removes vertices along the
# spine *even* if they are part of an edge that is outside the spine.
pruned2=prune_vertices(Cell07PNs[[1]], spine_ids)