Make sure given root IDs look like CRANT root IDs

If x is a single character query (e.g. "/cell_type:ExR1" or "/super_class:descending"), it is looked up in the CRANTb seatable via crant_meta() and the matching root ids are returned. Set normalise_colnames = TRUE to enable coconat-style aliases such as "/type:ExR1", "class:descending", or a bare type name like "ExR1". Otherwise validation is delegated to fafbseg::flywire_ids().

Usage

crant_ids(
  x,
  integer64 = NA,
  unique = FALSE,
  normalise_colnames = FALSE,
  na.rm = FALSE
)

Arguments

x

A character or bit64::integer64 vector or a dataframe specifying ids, or a single character query (see description).

integer64

Whether to return ids as 64 bit integers rather than character vectors. Default value of NA leaves the ids unmodified.

unique

For query inputs only, whether to drop rows with duplicate root ids (passed to crant_meta()). Ignored for non-query inputs.

normalise_colnames

Logical; if TRUE, pass normalise_colnames = TRUE to crant_meta() so query aliases such as class:/type: and bare type tokens are translated to the underlying seatable schema before lookup.

na.rm

Whether to drop missing (NA) root ids rather than returning them as the null segment "0" (passed to fafbseg::flywire_ids()). CRANTb_meta contains some incomplete rows with no root id.

Examples

if (FALSE) { # \dontrun{
# all descending neuron root ids
crant_ids("/super_class:descending")
# a specific cell type, as integer64
crant_ids("/cell_type:MDN", integer64 = TRUE)
# coconat-friendly query aliases (requires normalise_colnames = TRUE)
crant_ids("/class:descending", normalise_colnames = TRUE)
# a bare type name, likewise treated as a cell_type/type query
crant_ids("ExR1", normalise_colnames = TRUE)
} # }