check_duplicate_synapses: Check a neuron for potential duplicate synapses

Description Usage Arguments Details Value

View source: R/utils.R

Description

Given a neuron or skeleton ID, this function will look for outgoing connectors that are close enough to represent the same synapse. The function will return a data frame (optionally written to a CSV) with IDs of the identified connector pairs, their distances, and URLs to the connectors in CATMAID.

Usage

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check_duplicate_synapses(neuron = NULL, skid = NULL, xy_threshold = 200,
  z_threshold = 200, fileout = NULL)

Arguments

neuron

A CATMAID neuron object; required if skid is not provided.

skid

The skeleton ID of a neuron in CATMAID; required if neuron is not provided. Will only be used if neuron is not provided.

xy_threshold

The maximum X-Y distance (in the same units as your neuron) between two connectors for them to be considered potential duplicates. Defaults to 200.

z_threshold

The maximum Z distance (in the same units as your neuron) between two connectors for them to be considered potential duplicates. Defaults to 200.

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 data frame containing the connector ID of each connector in a pair, a CATMAID URL for each, the X-Y and Z distances between the connectors, and the skeleton ID of the neuron.


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