R+Shiny: read file and use its content

Question

Please find below an example of a script I found online (probably from Rstudio) to create a simple app to read a variety of flat files and output a table. I added a bit which creates the file "test_input_file.csv" which the app can read.

I am lost with a very simple task: after reading the csv file, I have a tibble and I render it as a table. How do I access this tibble directly to do something else with it? E.g. plot it with plotly, take some statistics etc...? Many thanks

library(shiny)
library(tidyverse)


tt <- tibble(AA=seq(10), BB=seq(10)*2, CC=seq(10)*3 )

write_csv(tt, "test_input_file.csv")

rm(tt)

# Define UI for data upload app ----
ui <- fluidPage(

  # App title ----
  titlePanel("Uploading Files"),

  # Sidebar layout with input and output definitions ----
  sidebarLayout(

    # Sidebar panel for inputs ----
    sidebarPanel(

      # Input: Select a file ----
      fileInput("file1", "Choose CSV File",
                multiple = FALSE,
                accept = c("text/csv",
                         "text/comma-separated-values,text/plain",
                         ".csv", "space")),

      # Horizontal line ----
      tags$hr(),

      # Input: Checkbox if file has header ----
      checkboxInput("header", "Header", TRUE),

      # Input: Select separator ----
      radioButtons("sep", "Separator",
                   choices = c(Comma = ",",
                               Semicolon = ";",
                               Tab = "\t",
                               Space = " "),
                   selected = ","),

      # Input: Select quotes ----
      radioButtons("quote", "Quote",
                   choices = c(None = "",
                               "Double Quote" = '"',
                               "Single Quote" = "'"),
                   selected = '"'),

      # Horizontal line ----
      tags$hr(),

      # Input: Select number of rows to display ----
      radioButtons("disp", "Display",
                   choices = c(Head = "head",
                               All = "all"),
                   selected = "head")

    ),

    # Main panel for displaying outputs ----
    mainPanel(

      # Output: Data file ----
      tableOutput("contents")

    )

  )
)

# Define server logic to read selected file ----
server <- function(input, output) {

  output$contents <- renderTable({

    # input$file1 will be NULL initially. After the user selects
    # and uploads a file, head of that data file by default,
    # or all rows if selected, will be shown.

    req(input$file1)

    # when reading semicolon separated files,
    # having a comma separator causes `read.csv` to error
    tryCatch(
      {
        df <- read.csv(input$file1$datapath,
                 header = input$header,
                 sep = input$sep,
                 quote = input$quote)
      },
      error = function(e) {
        # return a safeError if a parsing error occurs
        stop(safeError(e))
      }
    )

    if(input$disp == "head") {
      return(head(df))
    }
    else {
      return(df)
    }

  })

}

# Create Shiny app ----
shinyApp(ui, server)
#> PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.

Shiny applications not supported in static R Markdown documents

^{Created on 2022-03-09 by the reprex package (v2.0.1)}

Answer 1

This code loads the file straight into the output table and doesn't really store the raw table anywhere. This snippet of code is actually loading the file:

    df <- read.csv(input$file1$datapath,
                 header = input$header,
                 sep = input$sep,
                 quote = input$quote)

You can use this outside of the renderTable({}) to load the file just as a normal variable and do whatever you want with it.

However, if you set this code straight into the server function, it won't work - since this is a user input, you should set this variable as reactive, so I would do something like this:

  df = reactive({
    req(input$file1)
    
    df <- read.csv(input$file1$datapath,
                   header = input$header,
                   sep = input$sep,
                   quote = input$quote)
    
    return(df)
  })

Then you can call df() and do whatever you want with it. Ofc it would be nice to add try statements or some checks to make sure the file can be loaded properly, like the in the renderTable({}).

So the server side should look like this:

server <- function(input, output) {
  
  df = reactive({
    req(input$file1)
    
    df <- read.csv(input$file1$datapath,
                   header = input$header,
                   sep = input$sep,
                   quote = input$quote)
    
    return(df)
  })
  
  output$contents <- renderTable({
    
    # input$file1 will be NULL initially. After the user selects
    # and uploads a file, head of that data file by default,
    # or all rows if selected, will be shown.
    
    req(input$file1)
    
    # when reading semicolon separated files,
    # having a comma separator causes `read.csv` to error
    tryCatch(
      {
        df <- read.csv(input$file1$datapath,
                       header = input$header,
                       sep = input$sep,
                       quote = input$quote)
      },
      error = function(e) {
        # return a safeError if a parsing error occurs
        stop(safeError(e))
      }
    )
    
    if(input$disp == "head") {
      return(head(df))
    }
    else {
      return(df)
    }
    
  })
  
}