neuprint_dump: Download data from neuprint for specified bodyids / a...

In alexanderbates/neuprintr: R client utilities for interacting with the neuPrint connectome analysis service

Description

Download neuron morphology and connectivity data to a specified directrory as .csv and .rda files

Usage

neuprint_dump(dir, bodyids = NULL, roi = NULL, preprocess = NULL,
  connectivity = TRUE, volumes = TRUE, meta = TRUE, nat = TRUE,
  drvid = TRUE, soma = TRUE, heal = TRUE, connectors = TRUE,
  all_segments = TRUE, resample = FALSE, scale = 4,
  voxel.thresh = 1e+07, dataset = NULL, conn = NULL,
  OmitFailures = TRUE, ...)

Arguments

dir	the directory to which to save the dump
bodyids	the body IDs for neurons/segments (bodies) you wish to query
roi	a single ROI. Use neuprint_ROIs to see what is available.
preprocess	a function that can be applied to a nat::neuronlist object, to be called on neurons once they are read from the neuprint server using neuprint_read_neurons
connectivity	whether or not to include connectivity information in the dump, i.e. an adjacency matrix between bodyids
volumes	whether or not to include neuron volume information in the dump, i.e. voxels. Currently only works by talking to a DVID server using the package drvid
meta	whether or not to fetch a meta data for the given bodyids, using neuprint_get_meta
nat	whether or not to read neurons are nat::neuronlist objects (TRUE) or get SWC data frame (FALSE)
drvid	whether or not to use drvid::read.neuron.dvid rather than a cypher post request to neuprint_fetch_custom, in order to read a neuron. This might be faster, and this might also enable access to skeletons on an underlying DVID database that have not yet been ported to neuprint.
soma	whether or not to fetch a possible soma location for the given bodyids, using neuprint_locate_soma
heal	whether or not to heal a fragmented skeleton using a minimum spanning tree, via heal_skeleton
connectors	whether or not to add synapse data to the retrieved skeletons in the format used by the rcatmaid package, for easy use with rcatmaid or catnat functions. This can be done for synapse-less skeletons using neuprint_assign_connectors
all_segments	if TRUE, all bodies are considered, if FALSE, only 'Neurons', i.e. bodies with a status roughly traced status.
resample	if a number, the neuron is resampled using nat::resample, stepsize = resample. If 0 or FALSE (default), no resampling occurs.
scale	Resolution of sparse volume starting with 0 where each level beyond 0 has 1/2 resolution of previous level. "coarse" will return the volume in block coordinates.
voxel.thresh	the size threshold, in number of voxels, a neuron/segment must exceed, to be included in the dump, if read from an ROI
dataset	optional, a dataset you want to query. If NULL, the default specified by your R environ file is used. See neuprint_login for details.
conn	optional, a neuprintr connection object, which also specifies the neuPrint server see ?neuprint_login. If NULL, your defaults set in your R.profile or R.environ are used.
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an error. For other values, see details.
...	methods passed to neuprint_login

See Also

neuprint_get_synapses, neuprint_read_neurons

alexanderbates/neuprintr documentation built on May 28, 2019, 6:11 p.m.