flywire_partner_summary2: Rapid flywire connectivity summaries using cached connectome...

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Rapid flywire connectivity summaries using cached connectome data

Description

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()).

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

Value

A data.frame

Examples

## Not run: 
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)

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.