catmaid_get_connector_table: Return connector table for a given neuron

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

Return connector table for a given neuron

Description

Return connector table for a given neuron

Usage

catmaid_get_connector_table(
  skids,
  direction = c("both", "incoming", "outgoing"),
  partner.skids = TRUE,
  get_partner_names = FALSE,
  get_partner_nodes = FALSE,
  pid = 1,
  conn = NULL,
  raw = FALSE,
  ...
)

Arguments

skids	Numeric skeleton ids
direction	whether to find incoming or outgoing connections
partner.skids	Whether to include information about the skid of each partner neuron (NB there may be multiple partners per connector)
get_partner_names, get_partner_nodes	Whether to fetch the names and/or number of nodes for the partner neurons.
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.
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

Value

As of CATMAID v2016.10.18 this returns a data.frame with columns

• skid

• connector_id

• x

• y

• z

• confidence

• user_id

• treenode_id (NB this is always the treenode id of the query skeleton whether or not incoming or outgoing connections are requested)

• last_modified

• partner_skid

Prior to this it returned a data.frame with columns

• connector_id

• partner_skid

• x

• y

• z

• s

• confidence

• tags

• nodes_in_partner

• username

• treenode_id

• last_modified

See Also

Other connectors: catmaid_adjacency_matrix(), catmaid_get_connectors_between(), catmaid_get_connectors(), catmaid_query_connected(), connectors()

Examples

## Not run: 
# fetch connector table for neuron 10418394
ct=catmaid_get_connector_table(10418394)
# compare number of incoming and outgoing synapses
table(ct$direction)

## Look at synapse location in 3d
# plot the neuron skeleton in grey for context
library(nat)
nopen3d()
plot3d(read.neurons.catmaid(10418394), col='grey')
# note use of nat::xyzmatrix to get xyz positions from the ct data.frame
# colour synapses by direction
points3d(xyzmatrix(ct), col=as.integer(ct$direction))

## plot connected neurons in context of brain
nopen3d()
# fetch and plot brain model
models=catmaid_fetch("1/stack/5/models")
vs=matrix(as.numeric(models$cns$vertices), ncol=3, byrow = TRUE)
points3d(vs, col='grey', size=1.5)

# fetch and plot neurons
plot3d(read.neurons.catmaid(10418394), col='black', lwd=3)
points3d(xyzmatrix(ct), col=as.integer(ct$direction))

partner_neuron_ids=unique(na.omit(as.integer(ct$partner_skid)))
partner_neurons=read.neurons.catmaid(partner_neuron_ids, .progress='text', OmitFailures = TRUE)
plot3d(partner_neurons)

## End(Not run)

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