fanc_partner_summary: Summarise the connectivity of FANC neurons

In flyconnectome/fanc: Support Access to the Female Adult Nerve Cord (FANC) Dataset

Summarise the connectivity of FANC neurons

Description

fanc_partners returns details of each unitary synaptic connection (including its xyz location).

Usage

fanc_partner_summary(
  rootids,
  partners = c("outputs", "inputs"),
  threshold = 0,
  remove_autapses = TRUE,
  cleft.threshold = 0,
  datastack_name = NULL,
  ...
)

fanc_partners(rootids, partners = c("input", "output"), ...)

Arguments

rootids	Character vector specifying one or more flywire rootids. As a convenience this argument is passed to fanc_ids allowing you to pass in data.frames, flywire URLs or simple ids.
partners	Whether to fetch input or output synapses or both.
threshold	For flywire_partner_summary only return partners with greater than this number of connections to the query neuron(s) (default of 0 returns all connections)
remove_autapses	For flywire_partner_summary whether to remove autapses (defaults to TRUE)
cleft.threshold	A threshold for the cleft score calculated by Buhmann et al 2019 (default 0, we have used 30-100 to increase specificity)
datastack_name	An optional CAVE datastack_name. If unset a sensible default is chosen.
...	Additional arguments passed to pbsapply

Details

note that the rootids you pass in must be up to date. See example.

Value

a data.frame

See Also

flywire_partner_summary, fanc_latestid

Examples

# NB id must be up to date
sample_id=fanc_latestid("648518346481082458")
head(fanc_partner_summary(sample_id))
head(fanc_partner_summary(sample_id, partners='inputs'))
## Not run: 
# get the latest id for an outdate
fanc_partner_summary(fanc_latestid("648518346473954669"))

## open fanc/flywire scene containing top partners
library(dplyr)
fanc_partner_summary(fanc_latestid("648518346494405175"), partners='inputs') %>%
  slice_max(weight, n = 20) %>%
  fanc_scene(open=TRUE)

## End(Not run)
## Not run: 
# plot input and output synapses of a neuron
nclear3d()
fpi=fanc_partners(fanc_latestid("648518346481082458"), partners='in')
points3d(fanc_raw2nm(fpi$post_pt_position), col='cyan')
fpo=fanc_partners(fanc_latestid("648518346481082458"), partners='out')
points3d(fanc_raw2nm(fpo$pre_pt_position), col='red')

## End(Not run)

flyconnectome/fanc documentation built on Sept. 6, 2024, 9:56 a.m.