open_amira: Open a file or R object in Amira

In jefferis/nat.amira: Interface Between NeuroAnatomy Toolbox and Amira Visualisation Software

Description

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

Usage

## Default S3 method:
open_amira(x = NULL, ...,
  amira = getOption("nat.amira.amira", "Amira"), Verbose = FALSE)

open_amira(x = NULL, ...)

## S3 method for class 'neuron'
open_amira(x, ...)

## S3 method for class 'neuronlist'
open_amira(x, ...)

## S3 method for class 'matrix'
open_amira(x, ...)

## S3 method for class 'data.frame'
open_amira(x, ...)

## S3 method for class 'hxsurf'
open_amira(x, ...)

Arguments

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=FALSE, setting TRUE may help to debug connections)

Details

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.

See Also

write_neurons_for_amira

Examples

## 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)

## End(Not run)

jefferis/nat.amira documentation built on Aug. 11, 2019, 9:56 a.m.