catmaid_get_compact_skeleton: Return the raw data for a CATMAID neuronal skeleton

In jefferis/rcatmaid: R access to the API for the CATMAID web image annotation tool

Return the raw data for a CATMAID neuronal skeleton

Description

Return the raw data for a CATMAID neuronal skeleton

Usage

catmaid_get_compact_skeleton(
  skid,
  pid = 1L,
  conn = NULL,
  connectors = TRUE,
  tags = TRUE,
  raw = FALSE,
  ...
)

Arguments

skid	single skeleton id
pid	project id (default 1)
conn	the catmaid_connection object
connectors	Whether to fetch connector information
tags	Whether to fetch tag information
raw	Whether to return completely unprocessed data (when TRUE) or to convert the nodes and connectors lists into processed data.frames (when FALSE, the default)
...	Additional arguments passed to the catmaid_fetch function.

Details

Note that by default this fetches both skeleton and connector (synapse) information.

Value

An R list object with three elements

• nodes A data frame containing XYZ location, node identifiers etc for each point in the neuron.

• connectors A data frame containing the position and tree node identifiers for the synaptic partners.

• tags A list containing one vector for each named tag; the vectors contain node ids that are also present in the nodes element.

See Also

read.neuron.catmaid to read as neuroanatomy toolbox neuron that can be plotted directly. catmaid_fetch.

Examples

## Not run: 
## ensure that you have done something like
# conn=catmaid_login()
# at least once this session to connect to the server
skel=catmaid_get_compact_skeleton(10418394)
# no connector (i.e. synapse) information
skel=catmaid_get_compact_skeleton(10418394, connectors = FALSE)


## End(Not run)

jefferis/rcatmaid documentation built on Aug. 16, 2022, 8:52 p.m.