nat.templatebrains-package {nat.templatebrains} | R Documentation |
NeuroAnatomy Toolbox add-on package for handling template brains
Description
This package provides a class templatebrain
that stores key
information about reference brains along with helper functions to simplify
transformation of data between template brains (a.k.a bridging) and mirroring
of data within a template brain.
Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
Helper functions
Easy-to-use functions for transforming data from one template brain to another, displaying slices alongside 3D data, etc. are provided.
For transforming between spaces, see especially xform_brain
,
mirror_brain
. The regtemplate
functions allow
an R object containing neuroanatomical data to be tagged as in a particular
template brain space.
plot3d.templatebrain
provides a simple way to plot a surface
object representing a given template brain.
Registrations
Functions such as xform_brain
provided
by nat.templatebrains
are not very useful unless you tell the
package about bridging/mirroring registrations that you have available.
There are 4 supported ways to add registrations to the search list that
will be considered:
Install a package (e.g. nat.flybrains) that bundles registrations.
-
download_reg_repo
to download pre-packaged registration folders from github. This will automatically add the new folders to the registration search list both in the current session and on package startup. -
add_reg_folders
to add additional local directories to the registration search list. You will need to do this each time your start an R session unless you add it to yourRprofile
. -
add_reglist
to add an in-memoryreglist
containing an arbitrary sequence of registrations. By default this will not persist across R sessions but this behaviour can be changed.
Note that the package implements a cache to avoid rescanning the directories in the registration search list all the time. The functions mentioned above will automatically ensure that the cache is reset whenever a new set of registrations are added to the search list.
Package options
options('nat.templatebrains.regdirs') specifies a character vector of directories containing registrations i.e. a registration search list.
It is strongly recommended that you use the functions mentioned above rather than manipulating the registration search list directly.
Note that registration directories will be searched in the order that they are listed. It is therefore strongly recommended that individual registrations have globally unique names.
Author(s)
Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID)
Authors:
James Manton ajd.manton@googlemail.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/natverse/nat.templatebrains/issues
Examples
## Not run:
# Plot all known registrations
plot(bridging_graph(), vertex.size=25)
## manually add a new directory containing registrations to the search list
# Don't do this unless essential!
options(nat.templatebrains.regdirs=union(
getOption('nat.templatebrains.regdirs'), "/my/new/path"))
# NB after mucking around with paths manually you must also manually update
# the cache so that new registrations are actually used.
nat.templatebrains:::reset_cache()
## same, but override any built-in registration by putting the new path
# at the first position in the search list
options(nat.templatebrains.regdirs=union("/my/new/path"),
getOption('nat.templatebrains.regdirs'))
## End(Not run)