Get flywire IDs that map onto CATMAID neurons

Provide this function with a CATMAID query (skeleton IDs or an annotation term, as you could provide to catmaid::catmaid_skids) or a nat::neuronlist object in FAFB14 space, and it will return a ranked list of flywire IDs that map onto the given neuron(s).

Usage

fafb14_to_flywire_ids(
  search,
  only.root = FALSE,
  only.biggest = FALSE,
  pid = 1L,
  conn = NULL,
  fetch.annotations = FALSE,
  OmitFailures = FALSE,
  ...
)

Arguments

search

one or more skids or a CATMAID query expression. Else, a neuronlist of neurons in FAFB14 space.

only.root

only return one root_id at the location of the root node of the given CATMAID neuron(s)..

only.biggest

only return one root_id per CATMAID skid i.e. the biggest overlapping fragment.

pid

Project id (default 1)

conn

A catmaid_connection objection returned by catmaid_login. If NULL (the default) a new connection object will be generated using the values of the catmaid.* package options as described in the help for catmaid_login.

fetch.annotations

Whether or not to fetch the annotations for each skeleton (default FALSE)

OmitFailures

logical, whether to omit neurons that cannot be read from CATMAID.

...

Additional arguments passed to nat::nlapply.

Value

A data.frame of ranked flywire IDs, and the number of points in each CATMAID neuron that maps to that ID.

Examples

if (FALSE) {
# a specific skid
df=fafb14_to_flywire_ids(16)
head(df)

# Get neurons from a specific CATMAID environment
## See catmaid package help for  details on how to 'login'

# This is the Drosophila anatomy ontology identifier for DL1
# adult antennal lobe projection neuron DL1 adPN
# see \url{https://virtualflybrain.org} for details.
hits=fafb14_to_flywire_ids(search="FBbt:00067353", conn=catmaid::vfbcatmaid())
head(hits)
}