This is the repository for the Shiny application presented in "shinyCircos: an R/Shiny application for interactive creation of Circos plot" (Yu et al. Bioinformatics. 2017).
Help manual for the usage of shinyCircos [Download!]
shinyCircos is deployed at https://yimingyu.shinyapps.io/shinycircos/ and http://shinycircos.ncpgr.cn/ for online use.
shinyCircos is idle until you activate it by accessing the two URLs.
So it may take some time when you access this URL for the first time.
Once it was activated, shinyCircos could be used smoothly and easily.
User can choose to run shinyCircos installed locally for a more preferable experience.
Step 1: Install R and RStudio
Before running the app you will need to have R and RStudio installed (tested with R 3.3.3 and RStudio 1.0.143).
Please check CRAN (https://cran.r-project.org/) for the installation of R.
Please check https://www.rstudio.com/ for the installation of RStudio.
Step 2: Install the R Shiny package and other packages required by shinyCircos
Start an R session using RStudio and run these lines:
install.packages("shiny")
install.packages("circlize")
install.packages("RColorBrewer")
install.packages("data.table")
install.packages("RLumShiny")
# try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
Step 3: Start the app
Start an R session using RStudio and run these lines:
shiny::runGitHub("shinyCircos", "venyao")
Your web browser will open the app.
Step 1: Install R
Please check CRAN (https://cran.r-project.org/) for the installation of R.
Step 2: Install the R Shiny package and other packages required by shinyCircos
Start an R session and run these lines in R:
install.packages("shiny")
install.packages("circlize")
install.packages("RColorBrewer")
install.packages("data.table")
install.packages("RLumShiny")
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
For more information, please check the following pages:
https://cran.r-project.org/web/packages/shiny/index.html
https://github.com/rstudio/shiny
https://shiny.rstudio.com/
Step 3: Install Shiny-Server
Please check the following pages for the installation of shiny-server.
https://www.rstudio.com/products/shiny/download-server/
https://github.com/rstudio/shiny-server/wiki/Building-Shiny-Server-from-Source
Step 4: Upload files of shinyCircos
Put the directory containing the code and data of shinyCircos to /srv/shiny-server.
Step 5: Configure shiny server (/etc/shiny-server/shiny-server.conf)
# Define the user to spawn R Shiny processes
run_as shiny;
# Define a top-level server which will listen on a port
server {
# Use port 3838
listen 3838;
# Define the location available at the base URL
location /shinycircos {
# Directory containing the code and data of shinyCircos
app_dir /srv/shiny-server/shinyCircos;
# Directory to store the log files
log_dir /var/log/shiny-server;
}
}
Step 6: Change the owner of the shinyCircos directory
$ chown -R shiny /srv/shiny-server/shinyCircos
Step 7: Start Shiny-Server
$ start shiny-server
Now, the shinyCircos app is available at http://IPAddressOfTheServer:3838/shinycircos/.