WIlsON: Webbased Interactive Omics visualizatioN - The Application
Abstract
This repository contains the reference application of the WIlsON R package, 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.
Get a Docker container here.
The underlying WIlsON R package can be downloaded here.
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 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.