Shiny

• A web application framework for R

URLs

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

= Presentation =

Via `~/public_html`

• Ask for an personal Homepage.

• In ~/public_html create one folder for each shiny app and copy your R scripts to it.

  • Grant access to your files (only necessary if you created new files): Execute  setwww  in a linux console.

• URL: http://shiny.math.uzh.ch/user/<LASTNAME>/<FOLDER>/

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

iframe: Show the shiny app as a part of another page

• Put the following code on the page:

<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> 

An iframe simply displays another website in your website. With the style part of the command, you can customize the size of the frame.

• border: set the thickness of the border, the border color aswell 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, add left to one and right to the other.

Via gitlab deployment

• 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;
...

# Paket fehlt (Beispiel von SampleSizeR)
$ less /var/log/shiny-server-git/SampleSizeR-shiny-20230420-132522-42355.log
...
Error in library(ipc) : there is no package called ‘ipc’
...

# Überprüfen ob r-cran paket im ubuntu repo existiert
$ apt install r-cran-ipc

# Sonst Install über R
$ su - -c "R -e \"install.packages('ipc')\""

# Bei anderen Errors sollte der Code überprüft werden

# Am Ende vom Debugging sollte das persistent logging wieder deaktiviert werden, da sonst sehr viele logs entstehen

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)
  )
  ```