README.md
In jefferis/nat.as: NAT: Wrapper for informal neuroanatomy AnalysisSuite codebase

Introduction

This package is a thin wrapper around the AnalysisSuite that I have been using for a number of years to analyse and visualise 3D biological image data, especially neuronal structures. The idea is that this will immediately make it rather easier to install AnalysisSuite and that over time it should be possible to migrate many of the AnalysisSuite functions (currently in a loose bundle of R source code files and associated data) into a formal R package that I am incubating at nat.

Quick Start

For the impatient ...

# install
if(!require('devtools')) install.packages('devtools')
devtools::install_github('jefferis/nat')
devtools::install_github('jefferis/nat.as')
nat.as::install_analysis_suite()
nat.as::reload_analysis_suite()

# now use it
library(nat.as)
plot3d(kcs20,col=type)
?nat.as
?nat

Installation Details

There are 2 modes of installation increasing in order of difficulty and flexibility. If you just want to try things out, go with option 1. If you want to keep up to date regularly/hack on the AnalysisSuite code go with option 2, Developer Install (this is what I recommend for the lab).

devtools Install of Latest Version
Developer Install of Latest Version

The easiest approach to install the latest development version of the package + AnalysisSuite code from github as described in the Quick Start section above. However see below for the Developer install if you become a regular user and frequently update AnalysisSuite.

This is recommended both if you want to hack the AnalysisSuite code but also if you simply want to keep the code up to date regularly with git

First at the terminal:

# or some other directory you like
cd ~/projects
git clone https://github.com/jefferis/AnalysisSuite.git

Then in R:

library(nat.as)
install_analysis_suite("~/projects/AnalysisSuite")

To update the AnalysisSuite code (which is under regular development):

cd ~/projects/AnalysisSuite
git pull

Back in R if you want to hack on the AnalysisSuite code

library(nat.as)
# spot a bug
# hack code
reload_analysis_suite()
# test
test_analysis_suite()

Developing the nat.as Package

In the rare case that you want to checkout a version of the nat.as wrapper package that can be used for development (e.g. with Rstudio)

cd /some/suitable/dir
git clone https://github.com/jefferis/nat.as.git
# git clone jgit:nat.as # or local repository

cd /some/suitable/dir
git clone https://github.com/jefferis/AnalysisSuite
# git clone jgit:AnalysisSuite # or local repository

In R

install.packages('devtools') # install hadley's devtools
library(devtools)
load_all('/some/suitable/dir/nat.as')
#hack
check()
test()
load_all()

# check interaction with AnalysisSuite
document(); install()
install_analysis_suite('~/projects/AnalysisSuite/'); reload_analysis_suite()

# ready for release
check()
build_win() # test for Windows
release()
# or
library(gjdevtools)
gjrelease()