shinyChromosome: interactive creation of non-circular whole genome diagram





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Usage and installation of shinyChromosome

This is the repository for the Shiny application presented in “shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes” (Yu et al. Genomics Proteomics Bioinformatics. 2020).

Use shinyChromosome online

shinyChromosome is deployed at https://venyao.xyz/shinyChromosome/, https://venyao.shinyapps.io/shinyChromosome/ and https://yimingyu.shinyapps.io/shinychromosome/ for online use.
shinyChromosome is idle until you activate it by accessing the URLs.
So, it may take some time when you access this URL for the first time.
Once it was activated, shinyChromosome could be used smoothly and easily.

Launch shinyChromosome directly from R and GitHub

User can choose to run shinyChromosome installed on local computers (Windows, Mac or Linux) 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 3.5.0 and RStudio 1.1.419).
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 shinyChromosome

Start an R session using RStudio and run these lines:

# try an http CRAN mirror if https CRAN mirror doesn't work
install.packages("shiny")
install.packages("rlang")
install.packages("zip")
install.packages("ggplot2")
install.packages("plyr")
install.packages("ggthemes")
install.packages("RLumShiny")
install.packages("RColorBrewer")
install.packages("gridExtra")
install.packages("reshape2")
install.packages("data.table")
install.packages("shinythemes")
install.packages("shinyBS")
install.packages("markdown")
# install shinysky  
install.packages("devtools")  
devtools::install_github("venyao/ShinySky", force=TRUE)

Step 3: Start the app

Start an R session using RStudio and run these lines:

shiny::runGitHub("shinyChromosome", "venyao")

This command will download the code of shinyChromosome from GitHub to a temporary directory of your computer and then launch the shinyChromosome app in the web browser. Once the web browser was closed, the downloaded code of shinyChromosome would be deleted from your computer. Next time when you run this command in RStudio, it will download the source code of shinyChromosome from GitHub to a temporary directory again. This process is frustrating since it takes some time to download the code of shinyChromosome from GitHub.

Users are suggested to download the source code of shinyChromosome from GitHub to a fixed directory of your computer, such as ‘E:\apps’ on Windows. Following the procedure illustrated in the following figure, a zip file named ‘shinyChromosome-master.zip’ would be downloaded to the disk of your computer. Move this file to ‘E:\apps’ and unzip this file. Then a directory named ‘shinyChromosome-master’ would be generated in ‘E:\apps’. The scripts ‘server.R’ and ‘ui.R’ could be found in ‘E:\apps\shinyChromosome-master’.