Data analysis based on variables of a uploaded file OR the default dataset in R Shiny

Friday, May 25, 2018

Data analysis based on variables of a uploaded file OR the default dataset in R Shiny

Answer

I would like to make a Shiny app where the user can either upload their own rda/rds files or use the default datasets. The input selections choices will change depending on whether they want to use their down data or the default data.

E.g. in my code, I want the choices for mtbSelection to change depending on the values on the conditionalPanel.

I'm having trouble understanding how to load a .rda/.rds file in the server function and I'm not sure why the updateSelectInput doesn't work. Any help would be appreciated!

library(shiny)
library(shinythemes)

ui <- fluidPage(
  theme = shinytheme("paper"),
  checkboxInput("default_data", "Would you like to use default datasets?", value = TRUE),

  conditionalPanel(condition = "input.default_data == true",

                   selectizeInput(inputId = "mtb2", label = "Please choose a metabolomic dataset",
                                  choices = "mtb2",
                                  options = list(placeholder = 'Select a default metabolomic file below',onInitialize = I('function() { this.setValue(""); }'))
                   ),
                   selectizeInput(inputId = "geneExp2", label = "Please choose a transcriptome dataset",
                                  choices = "geneExp2",
                                  options = list(placeholder = 'Select a default transcriptome file below',onInitialize = I('function() { this.setValue(""); }'))
                   )
  ),
  conditionalPanel(condition = "input.default_data == false",

                   fileInput(inputId = "file_mtb", label = "Please upload a metabolomic dataset",
                             multiple = FALSE, accept = c('.RData', '.rda', '.rds'), placeholder = "  No file selected"
                   ),
                   fileInput(inputId = "file_ge", label = "Please upload a transcriptome dataset",
                             multiple = FALSE, accept = c('.RData', '.rda', '.rds'), placeholder = "  No file selected"
                   )


  ),


  selectInput("mtbSelection", strong("Select a metabolite of interest"), choices = "",
              multiple = FALSE)

)

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

  UploadMtbData <- reactive({
    infile <- input$file_mtb
    if (is.null(infile)){

      return()
    } else {
      return(readRDS(infile$datapath))
    }
  })

  observe({
    if (is.null(input$file_mtb)) #makes sure that the uploaded file is not null
      return()


    obj<-switch(input$file_mtb,
                 mtb2,
                 infile)

    var.opts <- colnames(obj)

    updateSelectInput(session, "mtbSelction", choices = var.opts)
  })




}

shinyApp(ui = ui, server = server)

Answer

Update: I updated the if statement. And very important the updateSelectInput was not working because of a typo!
Here is the code to generate the dummy data I used:

data(cars)

saveRDS(cars,'cars.rds')

I suggest the following server code (rest can stay as it is):

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

# reactive data
  mtbData <- reactive({
    # read default or user data

    if(input$default_data == TRUE || is.null(input$file_mtb)){
      # load your data here
    } else {
      # get input
      infile <- input$file_mtb
      # read and return
      readRDS(infile$datapath) 
    }
  })


  # update observer
  observe({
    # update
    updateSelectInput(session, "mtbSelection", choices = colnames(mtbData()))
  })

}

Blog

Friday, May 25, 2018