README.md

# WIlsON: Webbased Interactive Omics visualizatioN -  The Application
## Abstract
This repository contains the reference application of the [WIlsON R package]( https://github.molgen.mpg.de/loosolab/wilson), which is intended to provide HT screening results to the end user, either via a centralized R Shiny server, via applications such as Rstudio, or as a virtualized Docker container for offline usage. Please refer to that repository for a more detailed description. The WIlsON tool is a first step towards a user friendly and customizable omics result presentation that enables end users to generate high quality publication ready graphics without any programming skills.

## Availability
WIlsON can be tested on our [official demonstration server](http://loosolab.mpi-bn.mpg.de/apps/wilson/). 

Get a Docker container [here](https://hub.docker.com/r/loosolab/wilson/).

The underlying WIlsON R package can be downloaded [here](https://github.molgen.mpg.de/loosolab/wilson). 

Please make sure to check our other projects at http://loosolab.mpi-bn.mpg.de/.

## Installation of R Shiny server in “virgin” Debian 9 Linux
Update and install the following Debian packages.
```
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install r-base libnlopt-dev wget libssl-dev libxml2-dev libcurl4-openssl-dev git gdebi-core
```

Install **R Shiny server** according to the manual found here https://www.rstudio.com/products/shiny/download-server/ (make sure to install to global R library, NOT personal!).

Start R and install the **WIlsON R** package and dependencies (make sure to install to global R library, NOT personal!).
```
R
install.packages("devtools")
devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3")
```

Download the **WIlsON R application** archive from https://github.molgen.mpg.de/loosolab/wilson-apps and unzip. Move wilson-basic folder into R Shiny server apps folder (e.g. /srv/shiny-server/sample-apps/wilson-basic).

Change the owner of the R Shiny apps folder to be the “shiny” user.
```
sudo chown –R shiny:shiny /srv/shiny-server/sample-apps 
```

Restart R Shiny server.
```
sudo systemctl stop shiny-server
sudo systemctl daemon-reload
sudo systemctl start shiny-server
```

## Server structure
The R Shiny WIlsON application consists of the following components.
```
app.R		-> R code
/data		-> Folder with input file(s) (CLARION format)
/introduction	-> Introduction / Data Format web pages
/www		-> WIlsON logo
```

## How do I load my own data?
The [CLARION](http://loosolab.mpi-bn.mpg.de/apps/wilson/) format is explained in detail in the introduction of our official demonstration server. Add the file suffix *.clarion* or *.se*, and place it/them into the /data folder. Then you just have to reload the app or the server. That’s it! 
```
cp mydata.clarion /srv/shiny-server/sample-apps/data
sudo systemctl stop shiny-server
sudo systemctl daemon-reload
sudo systemctl start shiny-server
```

## Run app in RStudio
To run this app in your local RStudio you have to install the **WIlsON R package** and it's dependencies.
```
install.packages("devtools")
devtools::install_github(repo = "loosolab/wilson", host="github.molgen.mpg.de/api/v3")
```
Now either clone the repository and use ``runApp()``:
```
# Switch with setwd into the main folder e.g. wilson-apps.
setwd('yourPath'/wilson-apps)
# Use runApp to run the desired app. E.g. for wilson-basic
shiny::runApp("wilson-basic/")
```
Or use ``runUrl()``:
```
shiny::runUrl("https://github.molgen.mpg.de/loosolab/wilson-apps/archive/master.zip", subdir = "/wilson-basic")
```

## How to cite
* Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://XY

## License
This project is licensed under the MIT license.