lr.js

<script src="https://github.com/livereload/livereload-js/raw/master/dist/livereload.js?host=localhost"></script>

sage.js

<meta charset="utf-8">
<meta name="viewport" content="width=device-width">
<script src="http://aleph.sagemath.org/static/jquery.min.js"></script>
<script src="http://aleph.sagemath.org/static/embedded_sagecell.js"></script>
<script>
$(function () {
    sagecell.makeSagecell({inputLocation: 'div.compute-r',
                           evalButtonText: 'Evaluate',
                           defaultLanguage: "r", 
                           languages: sagecell.allLanguages});
});
</script>
<div class="compute-r"><script type="text/x-sage">
x <- 3 
x <- x + 3
print(x)
</script></div>

server.r

options(shiny.trace=TRUE, error = traceback)

shinyServer(function(input, output) {

  data_sets <- c("mymtcars","mtcars", "morley", "rock")
  mymtcars <- mtcars[,1:4]

  varnames <- function() {
    if(is.null(input$dataset)) return()

    dat <- get(input$dataset)
    colnames <- names(dat)

    return(colnames)
  }

  # if varnames is reactive only the data changes but the list of variable 
  # names is not updated
  # varnames <- reactive(varnames)

  changedata <- function() {
    dat <- get(input$dataset)
    dat[,1] <- NULL
    assign(input$dataset, dat, inherits = TRUE)
    # `<<-`('mymtcars', dat)      # this works
    # `<<-`(input$dataset, dat)   # this doesn't
    return()
  }

  # test
  changedata <- reactive(changedata)

  # Drop-down selection box for which data set
  output$choose_dataset <- reactiveUI(function() {
    selectInput("dataset", "Data set", data_sets)
  })

  # Check boxes
  output$choose_columns <- reactiveUI(function() {
    if(is.null(input$dataset))
      return()

    colnames <- varnames()

    # Create the checkboxes and select them all by default
    checkboxGroupInput("columns", "Choose columns", choices  = colnames, selected = colnames)
  })

  output$data1 <- reactiveText(function() {
    if(is.null(input$dataset) || is.null(input$columns))
      return()

    # if the changedata function is called here the data are updated 
    # but input_columns is not
    # print(varnames())
    # changedata()
    # print(varnames())

    # Get the data set
    dat <- get(input$dataset)

    # head(dat, 2)
    str(dat[1:2,])
  })

  # output$data2 <- reactiveTable(function() {
  output$data2 <- reactiveText(function() {
    if(is.null(input$dataset) || is.null(input$columns))
      return()

    # varnames are only updated if the varnames function is not reactive
    # data is changed for display in the data2 tab but not for data1 tab
    print(varnames())
    changedata()
    print(varnames())

    # Get the data set
    dat <- get(input$dataset)

    # head(dat, 2)
    str(dat[1:2,])
  })
})

ui.r

# Define UI for miles per gallon application
shinyUI(pageWithSidebar(

  headerPanel("Gist 4436657"),

	sidebarPanel(
		uiOutput("choose_dataset"),
		uiOutput("choose_columns")
	),

	mainPanel(
		includeHTML('lr.js'), # needed for livereload
		tabsetPanel(id = "analysistabs",
      tabPanel("Data1", verbatimTextOutput("data1")), 
      tabPanel("Data2", verbatimTextOutput("data2")),
      tabPanel("Sage", includeHTML('sage.js'))
		)
	)
))