write.neurons: Write neurons from a neuronlist object to individual files, or a zip archive

Description

Write neurons from a neuronlist object to individual files, or a zip archive

Usage

write.neurons(
  nl,
  dir,
  format = NULL,
  subdir = NULL,
  INDICES = names(nl),
  files = NULL,
  Force = FALSE,
  ...
)

Value

the path to the output file(s), absolute when this is a zip file.

Arguments

nl: neuronlist object
dir: directory to write neurons, or path to zip archive (see Details).
format: Unique abbreviation of one of the registered file formats for neurons including 'swc', 'hxlineset', 'hxskel'
subdir: String naming field in neuron that specifies a subdirectory OR expression to evaluate in the context of neuronlist's df attribute
INDICES: Character vector of the names of a subset of neurons in neuronlist to write.
files: Character vector or expression specifying output filenames. See examples and write.neuron for details.
Force: Whether to overwrite an existing file
...: Additional arguments passed to write.neuron

Author

jefferis

Details

See write.neuron for details of how to specify the file format/extension/name of the output files and how to establish what output file formats are available. A zip archive of files can be written by specifying a value of dir that ends in .zip.

Examples

Run this code

if (FALSE) {
# write some neurons in swc format
write.neurons(Cell07PNs, dir="testwn", format='swc')
# write some neurons in Amira hxlineset format
write.neurons(Cell07PNs, dir="testwn", format='hxlineset')

# organise new files in directory hierarchy by glomerulus and Scored.By field
write.neurons(Cell07PNs,dir="testwn",
  subdir=file.path(Glomerulus,Scored.By),format='hxlineset')
# ensure that the neurons are named according to neuronlist names
write.neurons(Cell07PNs, dir="testwn", files=names(Cell07PNs),
  subdir=file.path(Glomerulus,Scored.By),format='hxlineset')
# only write a subset
write.neurons(subset(Cell07PNs, Scored.By="ACH"),dir="testwn2",
  subdir=Glomerulus,format='hxlineset')
# The same, but likely faster for big neuronlists
write.neurons(Cell07PNs, dir="testwn3",
  INDICES=subset(Cell07PNs,Scored.By="ACH",rval='names'),
  subdir=Glomerulus,format='hxlineset')
# set file name explicitly using a field in data.frame
write.neurons(subset(Cell07PNs, Scored.By="ACH"),dir="testwn4",
  subdir=Glomerulus, files=paste0(ID,'.am'), format='hxlineset')
}

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