connectors: Get data.frame of connector (synapse) information from a...

In jefferis/rcatmaid: R access to the API for the CATMAID web image annotation tool

Get data.frame of connector (synapse) information from a neuron or neuronlist

Description

In contrast to catmaid_get_connector_table this assumes that you have already read the neurons into an R structure of class neuron or neuronlist.

Usage

connectors(x, ...)

## S3 method for class 'catmaidneuron'
connectors(x, ...)

## S3 method for class 'neuronlist'
connectors(x, subset = NULL, ...)

Arguments

x	Neuron or neuronlist
...	Additional arguments passed to methods (and to nlapply in the case of connectors)
subset,	optional subset of neurons to keep (see nlapply for details)

Details

Note that the id column identifying each neuron will be called bodyid or skid if such a field exists in the metadata attached to the neuron or id otherwise. If the column is called skid, the identifier will be converted to an integer otherwise it will be a character vector. These adjustments will avoid large 64 bit int ids from neuprint being zapped.

Value

A data.frame with columns

• treenode_id (NB this is the treenode id for the current skeleton)

• connector_skid

• prepost integer indicating whether connection is pre-(0) or post(1)-synaptic with respect to the current neuron. In other words this field will be 0 (pre) for the output synapses of this neuron.

• x Spatial Location

• y

• z

• skid For connectors.neuronlist, the skid of the skeleton from which connector information was retrieved.

See Also

nlapply

Other connectors: catmaid_adjacency_matrix(), catmaid_get_connector_table(), catmaid_get_connectors_between(), catmaid_get_connectors(), catmaid_query_connected()

Examples

## Not run: 
ornsl=read.neurons.catmaid("name:ORN left", OmitFailures = T, .progress='text')
conndf=connectors(ornsl)
summary(connectors(ornsl))

# plot points in 3d
library(nat)
nopen3d()
points3d(xyzmatrix(conndf), col=c(pre='red', post='cyan')[conndf$prepost+1])

## End(Not run)

jefferis/rcatmaid documentation built on Aug. 16, 2022, 8:52 p.m.