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Summarise the connectivity of CRANTb neurons

Source: R/partners.R
crant_partner_summary.Rd

Returns synaptically connected partners for specified neurons. Understanding synaptic partnerships is crucial for analyzing neural circuits in the CRANTb connectome.

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

Usage

crant_partner_summary(
  rootids,
  partners = c("outputs", "inputs"),
  synapse_table = c("synapses_v2"),
  threshold = 0,
  remove_autapses = TRUE,
  cleft.threshold = 0,
  datastack_name = NULL,
  version = NULL,
  timestamp = NULL,
  method = c("auto", "cave", "local"),
  ...
)

crant_partners(
  rootids,
  partners = c("input", "output"),
  synapse_table = c("synapses_v2"),
  version = NULL,
  timestamp = NULL,
  method = c("auto", "cave", "local"),
  ...
)

Arguments

rootids

Character vector specifying one or more crant rootids. As a convenience this argument is passed to crant_ids allowing you to pass in data.frames, crant URLs or simple ids.

partners

Character vector, either "input" or "output" to specify the direction of synaptic connections to retrieve.

synapse_table

Character, the name of the synapse CAVE table you wish to use. Defaults to the latest.

threshold

Integer threshold for minimum number of synapses (default 0).

remove_autapses

Logical, whether to remove self-connections (default TRUE).

cleft.threshold

Numeric threshold for cleft filtering (default 0).

datastack_name

An optional CAVE datastack_name. If unset a sensible default is chosen.

version, timestamp

A CAVE materialisation version or a timestamp (including "now") for the query. The default (both NULL) is the current time.

method

Whether to query CAVE or a local synapse snapshot (see crant_use_snapshot()). "auto" (the default) uses the selected local snapshot when there is one and the query can be answered from it, otherwise CAVE.

...

Additional arguments passed to flywire_partner_summary (CAVE queries only)

Value

a data.frame

Details

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

Local queries (method = "local") give the same results from a downloaded synapse snapshot without contacting CAVE for synapses, when the query time is no earlier than the snapshot. Edits made since the snapshot are fetched from CAVE (see crant_synapse_data()). They support the synapses_v2 table with cleft.threshold = 0 and the default datastack_name only.

See also

flywire_partner_summary, crant_latestid

Examples

if (FALSE) { # \dontrun{
# Basic connectivity analysis
sample_id=crant_latestid("576460752716912866")
head(crant_partner_summary(sample_id))
head(crant_partner_summary(sample_id, partners='inputs'))
} # }
if (FALSE) { # \dontrun{
# plot input and output synapses of a neuron
nclear3d()
fpi=crant_partners(crant_latestid("576460752716912866"), partners='in')
points3d(crant_raw2nm(fpi$post_pt_position), col='cyan')
fpo=crant_partners(crant_latestid("576460752716912866"), partners='out')
points3d(crant_raw2nm(fpo$pre_pt_position), col='red')
} # }