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Read neuronal skeletons via neuprint

Source: R/bodies.R
read_dyak_neurons.Rd

Read neuronal skeletons via neuprint

Usage

read_dyak_neurons(
  ids,
  connectors = FALSE,
  units = c("nm", "raw", "microns"),
  heal.threshold = Inf,
  conn = NULL,
  ...,
  dataset = dyak_default_dataset()
)

Arguments

ids

bodyids in any form compatible with malevnc::manc_ids().

connectors

Whether to fetch synaptic connections for the neuron (default FALSE in contrast to neuprintr::neuprint_read_neurons()).

units

Units of the returned neurons (default nm).

heal.threshold

The threshold for healing disconnected skeleton fragments. The default of Inf ensures that all fragments are joined together.

conn

Optional, a neuprint_connection object. Defaults to dyak_neuprint() to ensure that query is against the yakuba dataset.

...

Additional arguments passed to neuprintr::neuprint_read_neurons().

dataset

The name of the dataset as reported in Clio or neuprint.

Value

A nat::neuronlist object containing one or more neurons.

See also

malevnc::manc_read_neurons()

Examples

# \donttest{
dns <- read_dyak_neurons("DNa02")
#> Error in (function (path, body = NULL, server = NULL, conf = NULL, parse.json = TRUE,     include_headers = TRUE, simplifyVector = FALSE, app = NULL,     ...) {    if (is.null(app))         app = paste0("neuprintr/", utils::packageVersion("neuprintr"))    req <- if (is.null(body)) {        httr::GET(url = file.path(server, path, fsep = "/"),             config = conf, httr::user_agent(app), ...)    }    else {        httr::POST(url = file.path(server, path, fsep = "/"),             body = body, config = conf, httr::user_agent(app),             ...)    }    neuprint_error_check(req)    if (parse.json) {        parsed = neuprint_parse_json(req, simplifyVector = simplifyVector)        if (length(parsed) == 2 && isTRUE(names(parsed)[2] ==             "error")) {            stop("neuPrint error: ", parsed$error)        }        if (include_headers) {            fields_to_include = c("url", "headers")            attributes(parsed) = c(attributes(parsed), req[fields_to_include])        }        parsed    }    else req})(path = path, body = body, server = server, conf = conf, parse.json = parse.json,     include_headers = include_headers, simplifyVector = simplifyVector,     app = app): Unauthorized (HTTP 401). Failed to process url: https://neuprint-yakuba.janelia.org/api/dbmeta/datasets with neuPrint error: invalid or expired jwt.
dns
#> Error: object 'dns' not found
# }