RAVE

R Analysis and Visualization of ECOG Data

A. Installation

1. Environment Setup

In this section, you'll install R, RStudio, devtools and all other dependencies.

R is a functional programming language that RAVE uses. Devtools are necessary to enable advanced features. RStudio is an IDE (Intergrated Development Environment) for easy and better code management especially designed for R. If you are hosting a server in RAVE, or prefer to using command lines, RStudio is not necessary.

You need to check your operating system before installtion:

Mac OS
Windows (Windows 10, with Bash enabled)
Linux (Ubuntu-Like)
Linux (Others)

MacOS

First, go to Cran-R official website and download install the latest R:

https://cran.r-project.org/bin/macosx/

After installing R, make sure that you install Xcode from the Mac App Store:

The best way is to google How to install Xcode. Moncef Belyamani has a great article here.

Or if you have AFNI installed, you must have Xcode installed, then you need xcode command line tool. Open terminal (from Application), enter

xcode-select --install

RStudio

https://www.rstudio.com/products/rstudio/download/

Windows

On Windows, RAVE is limited because AFNI doesn't support windows. However, most of RAVE functions should work. To install RAVE, you need to have bash enabled on Windows 10.

It's easy to install on Windows.

First, go to Cran-R official website and download install the latest R:

https://cran.r-project.org/bin/windows/base/

After installing R, download and install Rtools. Please install the latest version:

https://cran.r-project.org/bin/windows/Rtools/

RStudio

https://www.rstudio.com/products/rstudio/download/

2. Install R dependencies and RAVE

If you have installed RStudio, open it, or if you are using terminal/command line, type R to enter R.

There are two ways to install RAVE.

2.1 If you want to install recommended version of RAVE (strongly recommended)

I have written a very simple and easy script for you. Open R, or RStudio, enter:

source('https://raw.githubusercontent.com/dipterix/instrave/master/R/hello.R')

If you fail, don't worry, try it several times, since there are so many packages to be installed and "turn R off and on again" is the easiest way to clean the installation environment :) However, if you try more than five times and still get errors, this might be an issue. Please report the issue on Github or contact me via my email.

Then you will see that RAVE is installed and attached. Type

init_app()

to enjoy :)

2.2 If you want to install specific version of RAVE

Inside of R, install devtools and rhdf5 by typing the following commands:

install.packages('devtools')
source("https://bioconductor.org/biocLite.R")
biocLite(c("rhdf5", "HDF5Array"), suppressUpdates = T, suppressAutoUpdate = T)

Next, install RAVE,

There are two versions of RAVE, Alpha, Beta version. To see the difference, please check RAVE updates

Alpha version (NOT recommended now)

This version was last updated at Dec/2017 and is no-longer supported. This version is only developed for Beauchamp's Lab. However, you can still see the demo here

devtools::install_github('beauchamplab/rave')

Please make sure that your R has packages devtools, tidyverse installed. It is also recommended that other packages (rhdf5, HDF5Array) be installed.

Beta Version

IMPORTANT: I'm Still maturing this version. However, it's runnable and contains more features than the alpha version. Please go to RAVE_dev-cycle to see the todo-list.

To install this version of RAVE, simply enter the following command:

devtools::install_github('beauchamplab/rave@rave-dipterix')

or -

devtools::install_github('beauchamplab/rave', ref = 'rave-dipterix')

Please make sure that you have latest yaml package installed. Upon failure, you might want to try: install.packages('yaml'). All other dependencies should be installed automatically

B. Toy example

Depending on the version of RAVE that you have installed

Beta version

Beta version is very easy. This version comes with some "real" data

To play with preprocess, type the following R command

rave_pre_process()

In the subject code, type Subject and press load button

To play with Main, type:

init_app()

Alpha version

If you have installed Alpha version, you can use the following code to launch

# Load packages
library(rave)
require(tidyverse)
require(magrittr)

# Re-direct ECOG data directory and module index file
rave_opts$set_options(
  data_dir = system.file('example/data', package='rave'),
  module_lookup_file = system.file('modules.csv', package='rave')
);

# Launch web service
init_app()

Please check vignettes/user_guide for details such as data format, SUMA connection, Matlab options. To know how to write modules, or use command lines (import subject data and perform quick analysis), check vignettes/rafe-cookbook.

xylimeng/rave