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()).

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. In order to use the data

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)
} # }