Using plots and data tables from Shiny app in R markdown report

Question

I have created a Shiny app, which involves the user importing data, manipulating it, creating a datatable and associated plot.

I'd like to build in a downloadable report using Rmarkdown (which I've only just started to use). However, i am unsure how to print the datatables and plots generated in R, in the Rmarkdown script, without copying the whole R code from the Shiny app. It is quite a long piece of code, so i'd like to be able to use the outputs directly.

As an example, I've copied the following app to demonstrate my point.

library(shiny)

ui <- fluidPage(

   titlePanel("Old Faithful Geyser Data"),

   sidebarLayout(
      sidebarPanel(
         sliderInput("bins",
                     "Number of bins:",
                     min = 1,
                     max = 50,
                     value = 30)
      ),

      mainPanel(
         plotOutput("distPlot"),
         dataTableOutput("summary_table"),
         downloadButton("report", "Generate report")
      )

   )
)

server <- function(input, output) {

   output$distPlot <- renderPlot({
      x    <- faithful[, 2] 
      bins <- seq(min(x), max(x), length.out = input$bins + 1)

      hist(x, breaks = bins, col = 'darkgray', border = 'white')
   })

   output$summary_table <- renderDataTable({
     x <- faithful
     head(x,5)
   })

   output$report <- downloadHandler(
     filename = "report.html",
     content = function(file) {
       tempReport <- file.path(tempdir(), "report.Rmd")
       file.copy("report.Rmd", tempReport, overwrite = TRUE)
       rmarkdown::render(tempReport, output_file = file,
                         envir = new.env(parent = globalenv())
       )
     }
   )
}

shinyApp(ui = ui, server = server)

I would like to access the plot and data table in my downloadable R markdown file.

Wimpel · Accepted Answer · 2017-10-23 12:37:19Z

1

my approach, using app.R and test.Rmd

in app.R create a reactive variable, containing the plot/chart (replace with your own plot).

chart1 <- reactive({
    ggmap(get_map(location = "Netherlands", 
                 zoom = 7, 
                 scale = 2, 
                 color="bw",
                 language = "nl-NL")) 
  })

then, call the markdown:

output$report <- downloadHandler(
filename = "test.pdf",

content = function(file) {
  src <- normalizePath('test.Rmd')

  #switch to system tempdir
  #just in case the app doesn't have write persission in the current folder
  owd <- setwd(tempdir())
  on.exit(setwd(owd))
  file.copy(src, 'test.Rmd', overwrite = TRUE)

  out <- render("test.Rmd", "pdf_document" )
  file.rename(out, file)
}

)

in the .Rmd file, you then can call on the chart:

plot(chart1())

Note the () after chart1!!!

Follow the same structure for tables, an all other objects you wish to include in your markdown..

answered Oct 23, 2017 at 12:37

Wimpel

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2 Comments

sym246 Over a year ago

I can't seem to implement the above, as my plotting code is wrapped in a renderPlotly function. Can I extract this sort of output?

Wimpel Over a year ago

I don't know. No experience with plotly.

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