open_amira.neuronlist and open_amira.neuron open
R neuronlist or neuron objects.
open_amira.matrix and open_amira.data.frame open a
set of 3D points as Amira landmark
open_amira.hxsurf opens a 3D surface mesh in Amira
# S3 method for default open_amira(x = NULL, ..., amira = getOption("nat.amira.amira", "Amira"), Verbose = FALSE) open_amira(x = NULL, ...) # S3 method for neuron open_amira(x, ...) # S3 method for neuronlist open_amira(x, ...) # S3 method for matrix open_amira(x, ...) # S3 method for data.frame open_amira(x, ...) # S3 method for hxsurf open_amira(x, ...)
| x | A file or object to open (optional) |
|---|---|
| ... | Additional arguments passed to methods |
| amira | Path to desired Amira version (see details) |
| Verbose | Whether or not to show the command line output from
communicating with Amira (default= |
When x is an R object, then a suitable file is written in a
temporary location on disk. For neuronlist objects, a script
object will also be generated in Amira that can be used to customise the
display of the neurons (toggle groups, colour, line width). See
write_neurons_for_amira and eventually
write.neurons for additional arguments you can set here.
Simply opens Amira if no file is specified. Presently only works on MacOS X.
Uses the package option otions('nat.amira.amira') to specify the path to Amira when this is set.
# NOT RUN { ## Open Amira open_amira() ## Load some scripts open_amira("myscript.scro") open_amira("mynetwork.hx") # Load some neurons and make checkboxes to turn on/off and colour by glomerulus # nb ... is passed to write_neurons_for_amira in this case open_amira(Cell07PNs, subdir=Glomerulus) # }