catmaid_adjacency_matrix: Get connectivity adjacency matrix between set of neurons

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

Get connectivity adjacency matrix between set of neurons

Description

Get connectivity adjacency matrix between set of neurons

Usage

catmaid_adjacency_matrix(
  inputskids,
  outputskids = inputskids,
  pid = 1,
  conn = NULL,
  ...
)

Arguments

inputskids, outputskids	Input (source) and output (target) skids in any form understandable to catmaid_skids.
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.
...	Additional arguments passed to the catmaid_fetch function

Value

A matrix, with inputs (sources) as rows and outputs (targets) as columns.

See Also

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

Examples

conn=vfbcatmaid('fafb')
da1adj=catmaid_adjacency_matrix("name:DA1", conn=conn)
# note that we translate skids to neuron names (longer but more informative)
heatmap(
  da1adj,
  scale = 'none',
  labCol = catmaid_get_neuronnames(colnames(da1adj)),
  labRow = catmaid_get_neuronnames(rownames(da1adj)),
  margins = c(12,12)
)

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