neuprint_get_paths: Get a list of paths of length n between 2 neurons

In natverse/neuprintr: R Client Utilities for Interacting with the neuPrint Connectome Analysis Service

Get a list of paths of length n between 2 neurons

Description

Get all of the paths in the database that connect the query neurons with at least weightT synapses at each step

Usage

neuprint_get_paths(
  body_pre,
  body_post,
  n,
  weightT = 5,
  roi = NULL,
  by.roi = FALSE,
  exclude.loops = TRUE,
  chunk = TRUE,
  progress = FALSE,
  dataset = NULL,
  conn = NULL,
  all_segments = FALSE,
  ...
)

Arguments

body_pre	the bodyid of the neuron at the start of the path
body_post	the bodyid of the neuron at the end of the path
n	the length of the path. If n is a vector, paths of length n[1] to n[2] are considered
weightT	weight threshold
roi	Limit the search to connections happening within a certain ROI or set of ROIs (NULL by default)
by.roi	Return the results by ROI. Default to FALSE
exclude.loops	Whether or not to exclude loops (paths containing the same node several times). Defaults to TRUE
chunk	A logical specifying whether to split the query into multiple chunks or an integer specifying the size of those chunks (which defaults to 5 when chunk=TRUE).
progress	if TRUE, a progress bar will be shown. This may slow the data fetching process for smaller queries. The default of progress=NULL will only show a progress bar if the query will be split into multiple chunks based on the chunk argument.
dataset	optional, a dataset you want to query. If NULL, the default specified by your R environ file is used or, failing that the current connection, is used. See neuprint_login for details.
conn	optional, a neuprintr connection object, which also specifies the neuPrint server. If NULL, the defaults set in your .Rprofile or .Renviron are used. See neuprint_login for details.
all_segments	if TRUE, all bodies are considered, if FALSE, only 'Neurons', i.e. bodies with a status roughly traced status.
...	methods passed to neuprint_login

See Also

neuprint_get_shortest_paths, neuprint_common_connectivity, neuprint_get_adjacency_matrix

Examples

neuprint_get_paths(c(1128092885,481121605),5813041365, n=c(1,2), weightT=20)

neuprint_get_paths(c(1128092885,481121605),5813041365, n=c(1,2),
  weightT=20,by.roi=TRUE)

neuprint_get_paths(c(1128092885,481121605),5813041365,
  n=c(1,2), weightT=20,roi=c("FB","LAL(-GA)(R)"))

natverse/neuprintr documentation built on Sept. 15, 2023, 6:59 a.m.