Vfrdtyky

I want to create an app with R shiny where I load data, display it and then I can make some operations on the data in another tibble/data frame and have the original data displayed in a tab. Additionally I would like to use the data in tibble cells to be used as the value for textInput. Thus far I have come up with this for the UI:

ui <- 

  dashboardPage(

    dashboardHeader(title="NGS library quantification app", titleWidth=500),

    dashboardSidebar(

    menuItem(text = "Raw Data", tabName = "r_data", icon=icon("clipboard")),

    menuItem(text = "User Data", tabName = "u_data", icon=icon("clipboard")),

    menuItem(text = "Analysis", tabName = "analysis", icon=icon("cog", lib = "glyphicon")),

    menuItem(text = "Summary", tabName = "summary", icon=icon("book")),

    collapsed=TRUE),

    dashboardBody(

      tags$head( 

        tags$style(HTML(".main-sidebar { font-size: 30px; }")) #change the font size to 30

      ),

      tags$script(

        HTML(

          "

                        $(document).ready(function(){

          // Bind classes to menu items, easiet to fill in manually

          var ids = ['r_data','u_data','analysis', 'summary'];

          for(i=0; i<ids.length; i++){

          $('a[data-value='+ids[i]+']').addClass('my_subitem_class');

          }



          // Register click handeler

          $('.my_subitem_class').on('click',function(){

          // Unactive menuSubItems

          $('.my_subitem_class').parent().removeClass('active');

          })

          })

          "

        )

        ),





      tabItems(

#Raw data tab              

tabItem(tabName = "r_data", fileInput(inputId = "file", label = "Choose file"), tableOutput("info"), tableOutput("raw_data")),



#user data tab

tabItem(tabName = "u_data",

            column(textInput("ID1", "Sample ID", value = ""),

                   textInput("ID2", "", value = ""),

                   textInput("ID3", "", value = ""),

                   textInput("ID4", "", value = ""),

                   textInput("ID5", "", value = ""),

                   textInput("ID6", "", value = ""),

                   textInput("ID7", "", value = ""),

                   textInput("ID8", "", value = ""),

                   width=1),  

            column(numericInput("size1", "library size (bp)", value = NULL, step=1), 

                        numericInput("size2", "", value = NULL, step=1),

                        numericInput("size3", "", value = NULL, step=1),

                        numericInput("size4", "", value = NULL, step=1),

                        numericInput("size5", "", value = NULL, step=1),

                        numericInput("size6", "", value = NULL, step=1),

                        numericInput("size7", "", value = NULL, step=1),

                        numericInput("size8", "", value = NULL, step=1),

                        width = 2),

              column(numericInput("dil1", "First dilution", value = 100000, step=10000), 

                     numericInput("dil2", "", value = 100000, step=10000),

                     numericInput("dil3", "", value = 100000, step=10000),

                     numericInput("dil4", "", value = 100000, step=10000),

                     numericInput("dil5", "", value = 100000, step=10000),

                     numericInput("dil6", "", value = 100000, step=10000),

                     numericInput("dil7", "", value = 100000, step=10000),

                     numericInput("dil8", "", value = 100000, step=10000),

                     width = 2),

              column(numericInput("dil9", "Second dilution", value = 250000, step=10000), 

                     numericInput("dil10", "", value = 250000, step=10000),

                     numericInput("dil11", "", value = 250000, step=10000),

                     numericInput("dil12", "", value = 250000, step=10000),

                     numericInput("dil13", "", value = 250000, step=10000),

                     numericInput("dil14", "", value = 250000, step=10000),

                     numericInput("dil15", "", value = 250000, step=10000),

                     numericInput("dil6", "", value = 250000, step=10000),

                     width = 2),

              column(numericInput("dil17", "Third dilution", value = 500000, step=10000), 

                     numericInput("dil18", "", value = 500000, step=10000),

                     numericInput("dil19", "", value = 500000, step=10000),

                     numericInput("dil20", "", value = 500000, step=10000),

                     numericInput("dil21", "", value = 500000, step=10000),

                     numericInput("dil22", "", value = 500000, step=10000),

                     numericInput("dil23", "", value = 500000, step=10000),

                     numericInput("dil24", "", value = 500000, step=10000),

                     width = 2),

              column(textInput("check1", "Sample Detected?", "YES"),

                     textInput("check2", "", "YES"),

                     textInput("check3", "", "YES"),

                     textInput("check4", "", "YES"),

                     textInput("check5", "", "YES"),

                     textInput("check6", "", "YES"),

                     textInput("check7", "", "YES"),

                     textInput("check8", "", "YES"),

                     width = 2) 

                    )

and then for the server:

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



# Reading data from CFX exported file      

    data <- reactive({

          inFile <- input$file

            if(is.null(inFile))

              return(NULL)



          data <- read_excel(paste(inFile$datapath), sheet=1, skip=18, col_types = c("text", "text", "text", 

                                                                                                      "text", "numeric", "numeric", "numeric", 

                                                                                              "numeric", "numeric"))

          })

ID1 <- reactive({data()[12, 2]})

updateTextInput(session, "ID1", value = reactive({ID1()}))  

}

Those are just snippets that I hope will be helpful with evaluating this problem. The problem is that when I then go back to the user data and look at the sample ID rather than seeing the ID of the sample I see what appears to be the code of the ID1 variable? I have no idea what I am doing wrong. I am new to Shiny and can't really troubleshoot this. you can find the app here

And this is the output in the textInput("ID1", "Sample ID", value = ""):

structure(function () ,{,    .dependents$register(),    if (.invalidated || .running) {,        ..stacktraceoff..(self$.updateValue()),    },    .graphDependsOnId(getCurrentContext()$id, .mostRecentCtxId),    if (.error) {,        stop(.value),    },    if (.visible) ,        .value,    else invisible(.value),}, observable = <environment>)

but I was expecting the value in the cell. Any help will be greatly appreciated. Thank you everyone

There are a few changes you need to make:

1. Put your updateTextInput inside an observer. This is because you need to read from a reactive expression, and observe does that.


2. You need to parse ID1() using as.character before being able to display it in your app.

Change your server to the following:

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



  # Reading data from CFX exported file      

  data <- reactive({

    inFile <- input$file

    if(is.null(inFile))

      return(NULL)



    data <- readxl::read_excel(paste(inFile$datapath), sheet=1, skip=18, 

                    col_types = c("text", "text", "text","text", "numeric", 

                    "numeric", "numeric","numeric", "numeric"))

  })



  ID1 <- reactive({data()[12, 2]})



  observe({

    updateTextInput(session, "ID1", value = as.character(ID1()))  

  })



}