r - Reading objects from shiny output object not allowed?

Question

I'm trying to write a little app that will allow the user to make a scatterplot, select a subset of points on the plot, then output a table in .csv format with just those selected points. I figured out how to get the page up and running and how to select points using brushedPoints. The table with selected points appears but when I press the Download button, the error "Reading objects from shinyoutput object not allowed." appears. Am I unable to download the table that I can visually see on the screen as a .csv? If so, is there a workaround?

I've recreated the problem using the iris dataset below. Any help figuring out why I cannot download the table of displayed rows would be greatly appreciated.

data(iris)

ui <- basicPage(
  plotOutput("plot1", brush = "plot_brush"),
  verbatimTextOutput("info"),mainPanel(downloadButton('downloadData', 'Download'))
)


server <- function(input, output) {
  output$plot1 <- renderPlot({
ggplot(iris,aes(x=Sepal.Width,y=Sepal.Length)) +
    geom_point(aes(color=factor(Species))) + 
    theme_bw()
  })

  output$info <- renderPrint({
brushedPoints(iris, input$plot_brush, xvar = "Sepal.Width", yvar = "Sepal.Length")
  })

  output$downloadData <- downloadHandler(
      filename = function() { 
        paste('SelectedRows', '.csv', sep='') },
        content = function(file) {
        write.csv(output$info, file)
      }
  )

}


shinyApp(ui, server)

Answer 1

The issue is that the output object is generating all of the web display stuff as well. Instead, you need to pull the data separately for the download. You could do it with a second call to brushedPoints in the download code. Better, however, is to use a reactive() function to do it just once, then call that everywhere that you need it. Here is how I would modify your code to make that work:

data(iris)

ui <- basicPage(
  plotOutput("plot1", brush = "plot_brush"),
  verbatimTextOutput("info"),mainPanel(downloadButton('downloadData', 'Download'))
)


server <- function(input, output) {
  output$plot1 <- renderPlot({
    ggplot(iris,aes(x=Sepal.Width,y=Sepal.Length)) + geom_point(aes(color=factor(Species))) + theme_bw()
  })


  selectedData <- reactive({
    brushedPoints(iris, input$plot_brush)
  })

  output$info <- renderPrint({
    selectedData()
  })

  output$downloadData <- downloadHandler(
    filename = function() { 
      paste('SelectedRows', '.csv', sep='') },
    content = function(file) {
      write.csv(selectedData(), file)
    }
  )

}


shinyApp(ui, server)

(Note, with ggplot2, you do not need to explicitly set xvar and yvar in brushedPoints. So, I removed it here to increase the flexibility of the code.)

I am not aware of any "lasso" style free drawing ability in shiny (though, give it a week -- they are constantly adding fun tools). However, you can mimic the behavior by allowing user to select multiple regions and/or to click on individual points. The server logic gets a lot messier, as you need to store the results in a reactiveValues object to be able to use it repeatedly. I have done something similar to allow me to select points on one plot and highlight/remove them on other plots. That is more complicated than what you need here, but the below should work. You may want to add other buttons/logic (e.g., to "reset" the selections), but I believe that this should work. I did add a display of the selection to the plot to allow you to keep track of what has been selected.

data(iris)

ui <- basicPage(
  plotOutput("plot1", brush = "plot_brush", click = "plot_click")
  , actionButton("toggle", "Toggle Seletion")
  , verbatimTextOutput("info")
  , mainPanel(downloadButton('downloadData', 'Download'))
)


server <- function(input, output) {
  output$plot1 <- renderPlot({

    ggplot(withSelected()
           , aes(x=Sepal.Width
                 , y=Sepal.Length
                 , color=factor(Species)
                 , shape = Selected)) +
      geom_point() +
      scale_shape_manual(
        values = c("FALSE" = 19
                   , "TRUE" = 4)
      , labels = c("No", "Yes")
      , name = "Is Selected?"
      ) +
      theme_bw()
  })

  # Make a reactive value -- you can set these within other functions
  vals <- reactiveValues(
    isClicked = rep(FALSE, nrow(iris))
  )


  # Add a column to the data to ease plotting
  # This is really only necessary if you want to show the selected points on the plot
  withSelected <- reactive({
    data.frame(iris
               , Selected = vals$isClicked)
  })



  # Watch for clicks
  observeEvent(input$plot_click, {

    res <- nearPoints(withSelected()
                      , input$plot_click
                      , allRows = TRUE)

    vals$isClicked <-
      xor(vals$isClicked
          , res$selected_)
  })


  # Watch for toggle button clicks
  observeEvent(input$toggle, {
    res <- brushedPoints(withSelected()
                         , input$plot_brush
                         , allRows = TRUE)

    vals$isClicked <-
      xor(vals$isClicked
          , res$selected_)
  })

  # pull the data selection here
  selectedData <- reactive({
    iris[vals$isClicked, ]
  })

  output$info <- renderPrint({
    selectedData()
  })

  output$downloadData <- downloadHandler(
    filename = function() { 
      paste('SelectedRows', '.csv', sep='') },
    content = function(file) {
      write.csv(selectedData(), file)
    }
  )

}


shinyApp(ui, server)