Set the DVID type, instance or group for some malecns neurons

Usage

mcns_set_dvid_annotations(
  ids,
  type = NULL,
  group = NULL,
  synonyms = NULL,
  side = NULL,
  instance = T,
  user = getOption("malevnc.dvid_user"),
  ...
)

Arguments

ids: Body ids
type: Character vector specifying an authoritative cell type e.g. "LHAD1g1" from the hemibrain.
group: One or more LR groups (i.e. candidate cell types) to apply. These should normally be the lowest bodyid of the group. Must be the same length as ids unless it has length 1.
synonyms: Character vector specifying cell type e.g. "LHAD1g1"
side: Character vector specifying the side of each neuron ("L", "R", "M" for midline, or "" when it cannot be specified).
instance: Character vector specifying instances (names) for neurons (see details) or a logical value where TRUE (the default) means to append the side to the type.
user: The DVID user. Defaults to options("malevnc.dvid_user").
...: Additional arguments passed to malevnc::manc_set_dvid_instance and thence to pbapply::pbmapply when there are multiple body ids.

Details

For the male CNS, the evolving standard seems to be to record the following fields (examples given for APL)

type='APL'
instance='APL_R'
group='APL_R'
type_user, instance_user, group_user='jefferisg' to accompany all of those.

Note that type_user, instance_user, group_user will be set automatically using the user argument. Regrettably you cannot currently specify different users for different different fields (e.g. one user for instance and a different user for type). Should you need to do this (e.g. when making annotations on behalf of other users) then you will need to make separate calls to mcns_set_dvid_annotations for each field you need set.

To delete an annotation set e.g. instance="". Be very careful!.

Examples

if (FALSE) { # \dontrun{
mcns_set_dvid_annotations(10297, type = 'LHAD1g1')
mcns_set_dvid_annotations(10977, type='APL', side='L', group = 10540)
# only set the LR group
mcns_set_dvid_annotations(ids=c(13115, 14424), group = 13115)

# unset i.e. remove a type (careful!)
mcns_set_dvid_annotations(18987, type = "", user = "becketti")
} # }