tagged_nodes: Generate URLs for specifically tagged nodes on a neuron

Description Usage Arguments Details Value

View source: R/utils.R

Description

Given a neuron and a particular tag, this will return a data frame (optionally written to a CSV) with the node IDs, coordinates, and CATMAID URLs.

Usage

1
2
3
tagged_nodes(neuron = NULL, tag, node.id = NULL,
  node.direction = c("downstream", "upstream"), volume = NULL,
  fileout = NULL)

Arguments

neuron

Required; a A CATMAID neuron object or skeleton ID.

tag

Required; a string specifying a tag.

node.id

Optional; the ID of a node at which to cut the neuron, if only a portion of the neuron should be considered.

node.direction

If a cut node is provided, which portion of the cut neuron to retain. Options are downstream (default) or upstream.

volume

Optional; a string specifying a FAFB neuropil to filter the tagged nodes.

fileout

Optional; the path to a CSV file where the result should be written.

Details

Requires the catmaid.server option to be set in .Rprofile

Value

A subset of the neuron's treenode data frame (d) including only tagges nodes, with a CATMAID URL for each.


fmlove/tracerutils documentation built on Oct. 22, 2018, 1:09 p.m.