flywire_dcvs: Get predicted dense core vesicle locations in the flywire...
In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

flywire_dcvs

R Documentation

Get predicted dense core vesicle locations in the flywire dataset

Description

Preliminary dense core vesicle (DCV) detection results from the Lee group, Stephan Gerhard and Minsu Kim.

Usage

flywire_dcvs(
  rootid,
  dataset = c("dcv.3.0", "dcv.2.0", "dcv.1.0"),
  project = "fruitfly_fafb_flywire",
  islatest = TRUE,
  simplify = TRUE,
  return = c("parsed", "text", "response"),
  token = NULL,
  simplifyVector = TRUE,
  include_headers = FALSE,
  OmitFailures = TRUE,
  cl = NULL,
  ...
)

Arguments

`rootid`	flywire rootid/rootids
`dataset`	which DCV data set from Stephan Gerhard to access. 1.0 is just for the antennal lobes of FAFB. 2.0 is the first run at the whole brain.
`project`	from which project to pull data. At the moment, there is only one option for DCV data.
`islatest`	logical, whether or not to fetch the latest root_id if the given IDs are out of date.
`simplify`	logical, if `FALSE` each rootid is a separate set of two data frames (one for DCV positions, one for the neuron's synapses). Else, a list of two combined data frames is returned.
`return`	One of "parsed", "text" (for raw JSON), or "response"
`token`	Optional chunkedgraph token (otherwise the default one for the current segmentation will be used). Use `NA` to suppress use of a token.
`simplifyVector`	Whether to use `jsonlite::simplifyVector`
`include_headers`	Whether to include basic headers from the http request as attributes on the parsed JSON object (default `TRUE`) when `parse.json=TRUE`.
`OmitFailures`	logical, if `TRUE` then requests that result in a 500 error are dropped and a warning is displayed but not an error.
`cl`	A cluster object created by `parallel::makeCluster`, or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations.
`...`	additional arguments passed to the `httr::{RETRY}` function. This may include a `config` list other named parameters etc.

Value

A list, where the first entry contains DCV locations and the second the synapses for the given rootid, with the nearest DCV precalculated for each synapse..

Examples

## Not run: 
# Just AL test data set
data = flywire_dcvs("720575940629166904", dataset = "dcv.1.0")
dcv = data$dcv
synapse = data$syns

# Whole brain data set
dcv = flywire_dcvs(c("720575940631973089","720575940629166904"), dataset = "dcv.2.0")

## End(Not run)

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