A general R Shiny module to import Comma or Tab Separated Files

fileImportModule.R

fileImportUI <- function(id, label = "Comma or Tab Separated File") {
  ns <- NS(id)
  
  tagList(
    # browse to select file to import
    fileInput(ns("selectedFile"), label, accept = c(
      "text/csv",
      "text/comma-separated-values",
      "text/plain",
      ".csv",
      ".tsv",
      ".txt"
    )),
    # checkbox to indicate if the original file has column headers
    checkboxInput(ns("hasColumnHeaders"), label = "Has column headers", value = TRUE),
    # combobox to specify quote type
    selectInput(ns("quoteType"), label = "Quote type", c(
      "None" = "",
      "Double quote" = "\"",
      "Single quote" = "'"
    )),
    # specify value separator
    selectInput(ns("separator"), label = "Separator type", c(
      "Comma" = ",",
      "Tab" = "\t"
    )),
    # server will provide options after parsing the table. 
    # this is to specify which column should be used as unique row names for R data frame
    uiOutput(ns("columnAsRowNamesControl")),
    # a preview table to help user get the right format
    box(title = "Data Preview",
        status = "primary",
        solidHeader = TRUE,
        collapsible = TRUE,
        width = 12,
        DT::dataTableOutput(ns("previewTable"))
    ),
    # the import button
    actionButton(ns("importButton"), "Import")
  )
}

fileImport <- function(input, output, session, stringsAsFactors = FALSE) {
  
  # user selected file
  verifiedSelectedFile <- reactive({
    validate(need(input$selectedFile, message = FALSE))
    input$selectedFile
  })
  
  # to give a correct list of column names, need to use NULL for param row.names
  tableColumnsOptions <- reactive({
    dataFrameWithAllColumnsAsData <- head(read.table(verifiedSelectedFile()$datapath,
                                                     header = input$hasColumnHeaders,
                                                     quote = input$quoteType,
                                                     sep = input$separator,
                                                     stringsAsFactors = stringsAsFactors,
                                                     row.names = NULL))
    colNames <- colnames(dataFrameWithAllColumnsAsData)
    tableColumns <- c(1 : length(colNames))
    names(tableColumns) <- colNames
    tableColumns
  })
  
  # render the preview table with actual imported data frame, using the specified param row.names
  output$previewTable <- DT::renderDataTable(head(instantDataFrame()), options = list(scrollX = TRUE))
  
  # render a combobox for user to select which column to use as row.names param
  output$columnAsRowNamesControl <- renderUI({
    # for server side defined UI element, has to retrieve ns function and wrap the input's id
    ns <- session$ns
    selectInput(ns("columnAsRowNames"),
                label = "Choose a column as unique row names",
                choices = tableColumnsOptions())
  })
  
  # the current data frame imported regarding to the use specified options
  instantDataFrame <- reactive({
    columnIndex <- input$columnAsRowNames
    # the selectinput ui gives a string rather than integer, so needs to be converted
    if (!is.null(columnIndex)) {
      columnIndex <- as.integer(columnIndex)
    }
    
    read.table(verifiedSelectedFile()$datapath,
               header = input$hasColumnHeaders,
               quote = input$quoteType,
               sep = input$separator,
               stringsAsFactors = stringsAsFactors,
               row.names = columnIndex)
  })
  # return the imported data only when the import button clicked
  dataToBeImported <- eventReactive(input$importButton, {
    instantDataFrame()
  })
  
  return(dataToBeImported)
}

global.R

library(shiny)
library(shinydashboard)
library(DT)

source("fileImportModule.R")

server.R

shinyServer(function(input, output) {
  importedData <- callModule(fileImport, "fileImport1")
  
  output$debug <- renderPrint({
    print(importedData())
  })
})

ui.R

dashboardPage(
  dashboardHeader(title = "File Importing Module Example"),
  dashboardSidebar(),
  dashboardBody(
    fluidRow(
      box(title = "Data Import",
          status = "primary",
          solidHeader = TRUE,
          width = 12,
          fileImportUI("fileImport1"),
          verbatimTextOutput("debug")
      )
    )
  )
)

All the required libraries are indicated in global.R