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

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

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', if no format can be extracted from the filename and the ext parameter, then it defaults to 'swc'

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

Value

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

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.

See also

Examples

if (FALSE) { # write some neurons in swc format write.neurons(Cell07PNs, dir="testwn", format='swc') # write some neurons in swc format for picky software write.neurons(Cell07PNs, dir="testwn", format='swc', normalise.ids=TRUE) # 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') }