Connectivity query for yakuba neurons

Connectivity query for yakuba neurons

Usage

dyak_connection_table(
  ids,
  partners = c("inputs", "outputs"),
  moredetails = c("class", "group", "type", "somaSide", "somaNeuromere", "hemilineage"),
  summary = FALSE,
  threshold = 1L,
  roi = NULL,
  by.roi = FALSE,
  conn = NULL,
  ...,
  dataset = dyak_default_dataset()
)

Arguments

ids

A set of body ids (see dyak_ids() for a range of ways to specify these).

partners

Either inputs or outputs. Redundant with prepost, but probably clearer.

moredetails

Either a logical (to add all fields when TRUE) or a character vector naming additional fields returned by dyak_neuprint_meta() that will be added to the results data frame.

summary

When TRUE and more than one query neuron is given, summarises connectivity grouped by partner.

threshold

Only return partners >= to an integer value. Default of 1 returns all partners. This threshold will be applied to the ROI weight when the roi argument is specified, otherwise to the whole neuron.

roi

a single ROI. Use neuprint_ROIs to see what is available.

by.roi

logical, whether or not to break neurons' connectivity down by region of interest (ROI)

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_connection_table().

dataset

The name of the dataset as reported in Clio e.g. yakuba, yakuba-vnc etc. yakuba, yakuba-vnc and yakubavnc are treated as aliases for the main yakuba dataset.

Value

A data frame.

See also

malevnc::manc_connection_table()

Examples

# \donttest{
dyak_connection_table("DNa02", partners = "outputs")
#> 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$error)        }        if (include_headers) {            fields_to_include = c("url", "headers")            attributes(parsed) = c(attributes(parsed), req[fields_to_include])        }        parsed    }    else req})(path = path, body = body, server = server, conf = conf, parse.json = parse.json,     include_headers = include_headers, simplifyVector = simplifyVector,     app = app): Unauthorized (HTTP 401). Failed to process url: https://neuprint-yakuba.janelia.org/api/dbmeta/datasets with neuPrint error: invalid or expired jwt.
dyak_connection_table("DNa02", partners = "outputs", summary = TRUE)
#> Error in (function (path, body = NULL, server = NULL, conf = NULL, parse.json = TRUE,     include_headers = TRUE, simplifyVector = FALSE, app = NULL,     ...) {    if (is.null(app))         app = paste0("neuprintr/", utils::packageVersion("neuprintr"))    req <- if (is.null(body)) {        httr::GET(url = file.path(server, path, fsep = "/"),             config = conf, httr::user_agent(app), ...)    }    else {        httr::POST(url = file.path(server, path, fsep = "/"),             body = body, config = conf, httr::user_agent(app),             ...)    }    neuprint_error_check(req)    if (parse.json) {        parsed = neuprint_parse_json(req, simplifyVector = simplifyVector)        if (length(parsed) == 2 && isTRUE(names(parsed)[2] ==             "error")) {            stop("neuPrint error: ", parsed$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.
# }