https://github.com/jefferis/nat.as

NAT: Wrapper for informal neuroanatomy AnalysisSuite codebase
https://github.com/jefferis/nat.as

Last synced: 27 days ago
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NAT: Wrapper for informal neuroanatomy AnalysisSuite codebase

• Host: GitHub
• URL: https://github.com/jefferis/nat.as
• Owner: jefferis
• Created: 2014-01-02T10:45:56.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2016-12-15T18:56:14.000Z (almost 8 years ago)
• Last Synced: 2023-04-16T09:10:56.730Z (over 1 year ago)
• Language: R
• Size: 46.9 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Introduction

============

This package is a thin wrapper around the [AnalysisSuite](https://github.com/jefferis/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](https://github.com/jefferis/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

  

devtools 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.

Developer Install of Latest Version

-----------------------------------

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()

Details

=======

For further information about this package see:

  * https://github.com/jefferis/AnalysisSuite

  * http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start