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Summarise the connectivity of banc neurons

Source: R/partners.R
banc_partner_summary.Rd

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

Usage

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

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

Arguments

rootids

Character vector specifying one or more BANC rootids. As a convenience this argument is passed to banc_ids allowing you to pass in data.frames, BANC 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

Value

a data.frame

Details

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

See also

flywire_partner_summary, banc_latestid

Examples

if (FALSE) { # \dontrun{
# NB id must be up to date
sample_id=banc_latestid("720575941478275714")
head(banc_partner_summary(sample_id))
head(banc_partner_summary(sample_id, partners='inputs'))
# get the latest id for an outdate
banc_partner_summary(banc_latestid("720575941478275714"))

## open banc/flywire scene containing top partners
library(dplyr)
banc_partner_summary(banc_latestid("720575941478275714"), partners='inputs') %>%
  slice_max(weight, n = 20) %>%
  banc_scene(open=TRUE)
} # }
if (FALSE) { # \dontrun{
# plot input and output synapses of a neuron
nclear3d()
fpi=banc_partners(banc_latestid("720575941478275714"), partners='in')
points3d(banc_raw2nm(fpi$post_pt_position), col='cyan')
fpo=banc_partners(banc_latestid("720575941478275714"), partners='out')
points3d(banc_raw2nm(fpo$pre_pt_position), col='red')
} # }