Shiny

The Shiny Server searches for R scripts in the folder it is pointed to and translates the shiny R script to normal HTML that any browser can read.

Turn your R script into a webpage

• Ask for a personal Homepage if you do not have one

• In ~/public_html create one folder for each shiny app and copy your R scripts there. Grant access to your files (only necessary if you created new files) by executing setwww in a linux console.

• URL to your app: http://shiny.math.uzh.ch/user/<NAME>/<FOLDER>/ where

  • NAME is typically your lastname, lowercase

  • FOLDER is the subfolder in public_html with the scripts

  Example: http://shiny.math.uzh.ch/user/doe/shinyapp1/

Show the shiny app as a part of another page

Use an iframe to embed your shiny app on another website as follows:

<iframe src="http://shiny.math.uzh.ch/user/doe/shinyapp1/" style="border: 1px solid #AAA; width: 290px; height: 500px">
  Your Browser doesn't support iframe
</iframe> 

With the style part of the command, you can customize the size and look of the frame:

• border: set the thickness of the border, the border color as well as the style it should be displayed in (solid, dotted, stripped). You can also deactivate the border completely by writing border: none;

• width: set a custom width to the frame. Normally very dependent on the app you load.

• height: set a height. Usually you just want the frame to be high enough that no scrollbar appears.

• float: You can let the frame float to either the left or right side of the text. If you want two iframes displayed side by side, use float: left on one and float: right on the other.

Deployment with gitlab-runner

• Example deployment: https://git.math.uzh.ch/bbaer/publish-shiny example .gitlab-ci.yml file.

• A commit to the GIT Repo will trigger the deployment described by .gitlab-ci.yml (via a gitlab-runner on alfred16, alfred20 or alfred22)

Debugging Apps

• Ask IT Support for sudo rights on the shiny server.

• Activate persistent logs:

  [root@shiny22]
  
  # Option einfügen unter zeile 'run_as shiny;'
  $ vim /etc/shiny-server/shiny-server.conf
  ...
  run_as shiny;
  
  preserve_logs true;
  ...

• Examine the log file for errors, for example a missing or an outdated package (an example from SampleSizeR)

  $ less /var/log/shiny-server-git/SampleSizeR-shiny-20230420-132522-42355.log
  ...
  Error in library(ipc) : there is no package called ‘ipc’
  ...
  Error : package or namespace load failed for ‘plotly’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace ‘vctrs’ 0.6.3 is already loaded, but >= 0.6.4 is required
  ...

  • the missing package exists in Ubuntu repo then it can be intalled directly

    $ sudo apt list | grep r-cran-ipc
    r-cran-vctrs/jammy,now 0.6.4-1cran1.2204.0 amd64
    $ sudo apt install r-cran-vctrs

    Otherwise it must be installed from within R:

    $ sudo "R -e \"install.packages('vctrs')\""

  • confirm the current version

    $ R -q -s -e "packageVersion('vctrs')"
    [1] ‘0.6.4’

• In case of other errors please check the R code

Important: persitent logs create huge log files - deactivate it when finished!

Samples

The samples displayed on http://shiny.math.uzh.ch page are the following

R Sample: Hello

The folder hello includes two files.

• server.R

  library(shiny)
  
  # Define server logic required to draw a histogram
  shinyServer(function(input, output) {
  
    # Expression that generates a histogram. The expression is
    # wrapped in a call to renderPlot to indicate that:
    #
    #  1) It is "reactive" and therefore should be automatically
    #     re-executed when inputs change
    #  2) Its output type is a plot
  
    output$distPlot <- renderPlot({
      x    <- faithful[, 2]  # Old Faithful Geyser data
      bins <- seq(min(x), max(x), length.out = input$bins + 1)
  
      # draw the histogram with the specified number of bins
      hist(x, breaks = bins, col = 'darkgray', border = 'white')
    })
  
  })

• ui.R

  library(shiny)
  
  # Define UI for application that plots random distributions
  shinyUI(pageWithSidebar(
  
    # Application title
    headerPanel("It's Alive!"),
  
    # Sidebar with a slider input for number of observations
    sidebarPanel(
      sliderInput("bins",
                    "Number of bins:",
                    min = 1,
                    max = 50,
                    value = 30)
    ),
  
    # Show a plot of the generated distribution
    mainPanel(
      plotOutput("distPlot", height=250)
    )
  ))

R Markdown Sample: rmd

The rmd Folder includes only one file:

• index.Rmd

  ---
  title: "Shiny Doc"
  output: html_document
  runtime: shiny
  ---
  
  ```{r, echo=FALSE}
  shinyApp(
  
    ui = fluidPage(
      selectInput("region", "Region:",
                  choices = colnames(WorldPhones)),
      plotOutput("phonePlot", height=270)
    ),
  
    server = function(input, output) {
      output$phonePlot <- renderPlot({
        barplot(WorldPhones[,input$region]*1000,
                ylab = "Number of Telephones", xlab = "Year")
      })
    },
  
    options = list(height = 345)
  )
  ```