Create selection list based on the column names of a csv file for plotting in Shiny

Question

I am trying to build a shiny app where I can upload a csv file and based on the column names, populate the check boxes on the left column (slidebar column) in ui. And based on which column selected for the y-axis and which column selected for the x-axis, need to able to create a chart using ggplot.

my ui.R looks like this:

shinyUI(pageWithSidebar(
  headerPanel("CSV Viewer"),
  sidebarPanel(
    fileInput('file1', 'Choose CSV File',
              accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
    tags$hr(),
    checkboxInput('header', 'Header', TRUE),
    radioButtons('sep', 'Separator',
                 c(Comma=',',
                   Semicolon=';',
                   Tab='\t'),
                 'Comma'),
    radioButtons('quote', 'Quote',
                 c(None='',
                   'Double Quote'='"',
                   'Single Quote'="'"),
                 'Double Quote'),

   checkboxGroupInput("variable", "Variable:", choices = names(data_set))
  ),
  mainPanel(
    tableOutput('contents')


  )
))

Server.R looks like this:

shinyServer(function(input, output) {
  output$contents <- renderTable({

    # input$file1 will be NULL initially. After the user selects and uploads a 
    # file, it will be a data frame with 'name', 'size', 'type', and 'datapath' 
    # columns. The 'datapath' column will contain the local filenames where the 
    # data can be found.

    inFile <- input$file1

    if (is.null(inFile))
      return(NULL)

    data_set<-read.csv(inFile$datapath, header=input$header, sep=input$sep, quote=input$quote)
  })

  output$choose_dataset <- renderUI({
    selectInput("dataset", "Data set", as.list(data_sets))
  })

  # Check boxes
  output$choose_columns <- renderUI({
    # If missing input, return to avoid error later in function
    if(is.null(input$dataset))
      return()

    # Get the data set with the appropriate name

    colnames <- names(contents)

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

})

I cannot get it to load column names in my data set in the slider bar? any pointers how I could do this. I am loading a csv file, once the file loaded, I need to be able to load populate the sliderbar with the column names of my dataset.

Update-edit:

added a request from OP (see comments in accepted answer) to read in a csv and select axes for plotting with ggplot. Added an additional answer for this as well.

Answer 1

This answer just fixes the csv loading problem, see my next answer below for one that actually does the plotting with ggplot.

So (after combining into one file to make it easier to work on), I added a checkboxGroupInput to the ui part and a corresponding updateCheckboxGroupInput to the server part. I needed it to update the group when the dataset changed, so I restructured the code a bit, making the data_set loading part a reactive encapsulating the updateCheckboxGroupInput inside an observer.

And so this does what you want:

library(shiny)
library(shinydashboard)
library(leaflet)
library(data.table)

ui <- pageWithSidebar(
  headerPanel("CSV Viewer"),
  sidebarPanel(
    fileInput('file1', 'Choose CSV File',
              accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
    tags$hr(),
    checkboxInput('header', 'Header', TRUE),
    checkboxGroupInput("inCheckboxGroup",
                       "Checkbox group input:",
                       c("label 1" = "option1",
                         "label 2" = "option2")),
    radioButtons('sep', 'Separator',
                 c(Comma=',',
                   Semicolon=';',
                   Tab='\t'),
                 ','),
    radioButtons('quote', 'Quote',
                 c(None='',
                   'Double Quote'='"',
                   'Single Quote'="'"),
                 '"'),
    uiOutput("choose_columns")
  ),
  mainPanel(
    tableOutput('contents')
  )
)

server <- function(input, output,session) {
  dsnames <- c()

  data_set <- reactive({
    req(input$file1)
    inFile <- input$file1
    data_set<-read.csv(inFile$datapath, header=input$header, 
                       sep=input$sep, quote=input$quote)
  })
  output$contents <- renderTable({
    data_set()
  })
  observe({
    req(input$file1)
    dsnames <- names(data_set())
    cb_options <- list()
    cb_options[ dsnames] <- dsnames
    updateCheckboxGroupInput(session, "inCheckboxGroup",
                             label = "Check Box Group",
                             choices = cb_options,
                             selected = "")
  })

  output$choose_dataset <- renderUI({
    selectInput("dataset", "Data set", as.list(data_sets))
  })

  # Check boxes
  output$choose_columns <- renderUI({
    # If missing input, return to avoid error later in function
    if(is.null(input$dataset))
      return()

    # Get the data set with the appropriate name

    colnames <- names(contents)

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

Here is a screenshot:

Answer 2

So adding another answer to accommodate an additional request - it not only reads in the file but and allows you to select columns for plotting, it actually does the plot in a separate tab with ggplot2:

library(shiny)
library(shinydashboard)
library(leaflet)
library(data.table)
library(ggplot2)

ui <- pageWithSidebar(
  headerPanel("CSV Viewer"),
  sidebarPanel(
    fileInput('file1', 'Choose CSV File',
              accept=c('text/csv','text/comma-separated-values,text/plain','.csv')),
    tags$hr(),
    checkboxInput('header', 'Header', TRUE),
    fluidRow(
      column(6,radioButtons("xaxisGrp","X-Axis:", c("1"="1","2"="2"))),
      column(6,checkboxGroupInput("yaxisGrp","Y-axis:", c("1"="1","2"="2")))
    ),
    radioButtons('sep', 'Separator',
                 c(Comma=',', Semicolon=';',Tab='\t'), ','),
    radioButtons('quote', 'Quote',
                 c(None='','Double Quote'='"','Single Quote'="'"),'"'),
    uiOutput("choose_columns")
  ),
  mainPanel(
    tabsetPanel(
      tabPanel("Plot",plotOutput("plot")),
      tabPanel("Data", tableOutput('contents'))
    )
  )
)
server <- function(input, output,session) {
  dsnames <- c()

  data_set <- reactive({
    inFile <- input$file1

    if (is.null(inFile))
      return(mtcars)

    data_set<-read.csv(inFile$datapath, header=input$header, 
                       sep=input$sep, quote=input$quote)
  })

  output$contents <- renderTable({data_set()})

  observe({
    dsnames <- names(data_set())
    cb_options <- list()
    cb_options[ dsnames] <- dsnames
    updateRadioButtons(session, "xaxisGrp",
                             label = "X-Axis",
                             choices = cb_options,
                             selected = "")
    updateCheckboxGroupInput(session, "yaxisGrp",
                             label = "Y-Axis",
                             choices = cb_options,
                             selected = "")
  })
  output$choose_dataset <- renderUI({
    selectInput("dataset", "Data set", as.list(data_sets))
  })
  output$plot = renderPlot(
    {
      df <- data_set()
      gp <- NULL
      if (!is.null(df)){
        xv <- input$xaxisGrp
        yv <- input$yaxisGrp
        if (!is.null(xv) & !is.null(yv)){
          if (sum(xv %in% names(df))>0){ # supress error when changing files
            mdf <- melt(df,id.vars=xv,measure.vars=yv)
            gp <- ggplot(data=mdf) + 
               geom_point(aes_string(x=xv,y="value",color="variable"))
          }
        }
      }
      return(gp)
    }
  )
  output$choose_columns <- renderUI({

    if(is.null(input$dataset))
      return()
    colnames <- names(contents)
    checkboxGroupInput("columns", "Choose columns", 
                       choices  = colnames,
                       selected = colnames)
  }) 
}
shinyApp(ui, server)

Yielding: