find_glomeruli: Finds the glomerulus associated with a PN

In flyconnectome/tracerutils: Utilities for EM Neuron Tracers

Description

Given a vector of skeleton IDs, this will find the glomerului associated with PNs, based on annotations in CATMAID.

Usage

find_glomeruli(skids, exclude = NULL, method = c("annotation", "name"),
  ...)

Arguments

skids	Required; an integer or character vector of skeleton IDs
exclude	Optional; a vector of glomeruli to exclude (in the format X for glomerulus X, or the full annotation for unknown glomerulus N)
method	Optional; indicating whether to use the neuron 'name' or glomerulus 'annotation's.
...	Additional arguments passed to catmaid_* functions. Use this to specify conn, pid or similar low level arguments for the catmaid_query.

Details

Requires the PN to be annotated with glomerulus X or unknown glomerulus N in CATMAID. Annotations of the form glomerulus X will be prioritised over unknown glomerulus N, and if there are multiples they will be joined together with a forward slash. If there are no results with either of these annotations, the string "unknown" will be returned in place of a glomerulus. Note that annotations of the form glomerulus X right|left are not considered.

Value

A character vector of glomeruli names

Examples

find_glomeruli('WTPN2017_uPN_right')
find_glomeruli('WTPN2017_uPN_right', exclude=c('VCx','VCy', 'VP1l'))
find_glomeruli('WTPN2017_uPN_right', method = 'name')

flyconnectome/tracerutils documentation built on May 6, 2020, 10:45 a.m.