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Return metadata about Aedes neurons from FlyTable

Source: R/meta.R
aedes_meta.Rd

By default aedes_meta() and aedes_ids() tell you exactly what is in FlyTable: its rows and root ids as stored there. Unlike most aedes functions they do not follow the aedes.version option (see aedes_set_version()). You can still time travel by giving a version (e.g. "latest") or a timestamp (e.g. "now"), which maps the root ids to that time.

Usage

aedes_meta(
  ids = NULL,
  ignore.case = FALSE,
  fixed = FALSE,
  version = NULL,
  timestamp = NULL,
  unique = FALSE,
  translate_ids = NA,
  expiry = 0,
  refresh = FALSE,
  ...
)

aedes_ids(
  ids,
  ignore.case = FALSE,
  fixed = FALSE,
  unique = FALSE,
  version = NULL,
  timestamp = NULL,
  expiry = 0,
  refresh = FALSE,
  ...
)

Arguments

ids

Root IDs (character/int64), a query string like "class:ALPN", a single string of comma/space-separated ids ("id1, id2, id3") or a neuroglancer URL (including shortened state URLs), from which the visible segments are used.

ignore.case

For query strings, whether to ignore case.

fixed

For query strings, whether to treat queries as fixed strings rather than regular expressions (default FALSE).

version

Optional CAVE materialisation version.

timestamp

Optional CAVE timestamp.

unique

Whether to drop duplicate root_id rows (with duplicates attached as an attribute).

translate_ids

Whether to bring explicitly supplied ids forward to the requested version/timestamp before matching (see Details). NA (the default) decides automatically.

expiry

Cache expiry in seconds passed to fafbseg::cam_meta(). Defaults to 0, always checking for updates so you see the latest metadata; set a positive value to trust the cache within that window, or Inf to use the on-disk cache without checking.

refresh

Logical passed to fafbseg::cam_meta(); if TRUE force a complete re-download of the table, ignoring any cache.

...

Additional arguments passed to fafbseg::cam_meta().

Value

For aedes_meta(), a data.frame of metadata. For aedes_ids(), a vector of root IDs.

Details

When version or timestamp are specified, root ids in the returned data frame will be mapped to the corresponding timepoint using the supervoxel_id column. When no version/timestamp is specified then ids will be simply as returned by the flytable (which updates them every half hour, so they can lag recent edits). If you want to be sure that ids match the most up to date state of the segmentation possible then you can ask for timestamp='now'.

For a query string the match happens against that mapped table, so no further work is needed. For explicit root ids the join is by root_id, so ids that are stale relative to the requested timepoint would silently fail to match. translate_ids guards against this by bringing the supplied ids forward with fafbseg::flywire_latestid() first. The default (NA) turns this on only when it is both needed and meaningful: explicit ids are supplied and a version/timestamp is given. With no version/timestamp nothing is translated, since the flytable is simply at the state of its last half-hourly update.

Examples

if (FALSE) { # \dontrun{
aedes_meta("class:ALPN")
aedes_ids("class:ALPN")

aedes_ids("class:ALPN", timestamp='now')
aedes_ids("class:ALPN", version='latest')
} # }