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Summarise the synaptic partners of one or more Aedes neurons

Source: R/partners.R
aedes_partner_summary.Rd

Tabulates the up- or downstream partners of a set of query neurons at a chosen CAVE materialisation, returning one row per partner with the number of connecting synapses. This is a thin Aedes-aware wrapper around fafbseg::flywire_partner_summary(): it resolves the input via aedes_ids(), points fafbseg at the Aedes segmentation, and updates root ids to the requested version/timestamp before querying.

Usage

aedes_partner_summary(
  rootids,
  partners = c("outputs", "inputs"),
  threshold = 0,
  version = NULL,
  timestamp = NULL,
  synapse_table = getOption("coconatfly.aedes.synapses", default = "synapses_v2"),
  ...
)

Arguments

rootids

Query neurons in any form accepted by aedes_ids() (root ids or a FlyTable query string).

partners

Whether to summarise "outputs" (downstream partners, the default) or "inputs" (upstream partners).

threshold

Only return partners connected by more than threshold synapses (default 0, i.e. all partners).

version, timestamp

Optional CAVE materialisation selectors. When supplied, query ids are first updated to the corresponding version / timestamp with fafbseg::flywire_latestid(), and the synapse query is run against that materialisation. Give at most one of the two.

synapse_table

CAVE synapse table to query. Defaults to the coconatfly.aedes.synapses option ("synapses_v2").

...

Additional arguments passed on to fafbseg::flywire_partner_summary(). Power-user options include remove_autapses (set FALSE to keep self-connections; see examples) and cleft.threshold.

Value

A data.frame with one row per partner neuron. query holds the query neuron root id and weight the synapse count; the partner root id is in post_id when partners = "outputs" and pre_id when partners = "inputs". See fafbseg::flywire_partner_summary() for the full column description.

See also

fafbseg::flywire_partner_summary(), aedes_ids()

Examples

if (FALSE) { # \dontrun{
# downstream partners of a neuron, keeping only strong connections
aedes_partner_summary("720575940...", threshold = 4)

# inputs instead of outputs
aedes_partner_summary("720575940...", partners = "inputs")

# Power-user: query a specific CAVE materialisation rather than 'now'
aedes_partner_summary("720575940...", version = 1000)
aedes_partner_summary("720575940...", timestamp = "2024-01-01")

# Power-user: include autapses (self-connections). MBON11 is strongly
# autaptic, so its own root id appears among its downstream partners when
# remove_autapses = FALSE (the fafbseg default drops these).
mbon11 <- aedes_ids("cell_type:MBON11")
aedes_partner_summary(mbon11, remove_autapses = FALSE)
} # }