Rapid flywire connectivity summaries using cached connectome data

Usage

flywire_partner_summary2(
  ids,
  partners = c("outputs", "inputs"),
  add_cell_types = TRUE,
  by.roi = FALSE,
  summarise = FALSE,
  threshold = 0,
  version = NULL
)

Arguments

ids: Root ids to query (passed to flywire_ids)
partners: Whether to fetch input or output synapses or both.
add_cell_types: Whether to add cell type information to the result
by.roi: Whether to break the connectivity down into rows for each neuropil region containing synapses.
summarise: Whether to collapse down the results for multiple query neurons into a single entry for each partner neuron.
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)
version: Optional CAVE version. The default value of NULL uses the latest data dump available unless options(fafbseg.flywire_connectome_data_version) has been set (which you can conveniently do using flywire_connectome_data_version()). The special version of "783.2" will use the 2025 (Princeton) synapse data release.

Value

A data.frame

Details

Note that the threshold is applied to each row left after any grouping operations. Therefore when by.roi=TRUE only neuropil regions exceeding this threshold will be returned.

CAVE specifies versions (effectively timestamps) for the connectome data. Every so often Sven makes a dump of the connectivity and synapse information for all proofread neurons. At this point, the only versions in use are 783 (released with the published articles in Nature) and 630 (released with the preprint).

The 783 release is available with both the original connectivity based on Buhmann et at 2021 (still the default) as well as new v2 synapses released in 2025 (version='783.2')

Examples

if (FALSE) { # \dontrun{
flywire_partner_summary2('DA2_lPN', partners='out')
flywire_partner_summary2('DA2_lPN', partners='out', summarise=T)
flywire_partner_summary2('DA2_lPN', partners='out', summarise=T, by.roi=T)

flywire_partner_summary2('DA2_lPN', partners='out', summarise=T,
  by.roi=T, add_cell_types=F) %>%
  filter(!grepl("AL", neuropil)) %>%
  group_by(post_pt_root_id) %>%
  summarise(weight = sum(weight), top_np = neuropil[1]) %>%
  arrange(desc(weight)) %>%
  # nb version = TRUE will use ensure that ids match the default CAVE version
  add_celltype_info(version=TRUE)
} # }