R/neuron-io.R
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, ...)
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 |
Force | Whether to overwrite an existing file |
... | Additional arguments passed to |
the path to the output file(s), absolute when this is a zip file.
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
.
write.neuron
, read.neurons
,
fileformats
Other neuronlist: *.neuronlist
,
is.neuronlist
,
neuronlist-dataframe-methods
,
neuronlistfh
, neuronlist
,
nlapply
, read.neurons
# NOT RUN { # 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') # }