Problem getting current list of input values in Shiny

Question

I'm having quite a few problems to get the updated values from several coonditionalPanels. I created a reactive variable parList which should contain the parN_sig input variables. These variables should come from conditional panels and they are all named parN_sig. I do not know why but I always end up getting values from the double_sig panel when another panel is shown at the UI.
Here's my code:
ui.r

jscode <- "
shinyjs.disableTab = function(name) {
  var tab = $('.nav li a[data-value=' + name + ']');
  tab.bind('click.tab', function(e) {
    e.preventDefault();
    return false;
  });
  tab.addClass('disabled');
}

shinyjs.enableTab = function(name) {
  var tab = $('.nav li a[data-value=' + name + ']');
  tab.unbind('click.tab');
  tab.removeClass('disabled');
}
"

css <- "
.nav li a.disabled {
  background-color: #aaa !important;
  color: #333 !important;
  cursor: not-allowed !important;
  border-color: #aaa !important;
}"
# Create Shiny object

library(shiny)
library(shinythemes)
library(shinyjs)
library(ggplot2)
library(grid)
library(egg)

# source("input.r")
source("functions.r")
formula_tabs<-tabsetPanel(
  tabPanel("double_sig",
           withMathJax("$$y=d+\\frac{a}{1+exp^{-b*(t-c)}}+\\frac{e}{1+exp^{-f*(t-g)}}$$")
  ),
  tabPanel("gompertz",
           withMathJax("$$y=b*exp^{\\ln(\\frac{c}{b})*exp^{-a*t}}$$")
  ),
  tabPanel("verhulst",
           withMathJax("$$y=\\frac{b*c}{b+(b-c)*exp^{-a*t}}$$")

  ),
  id = "formulas",
  type = "tabs"

)

fluidPage(useShinyjs(),theme = shinytheme("lumen"),useShinyjs(),tags$style("#params { display:none; } #formulas { display:none; }"),
          extendShinyjs(text = jscode),inlineCSS(css),
          navbarPage("Protein turnover model",id="tabs",
                     tabsetPanel(tabPanel("Input data",
                                          checkboxInput("multiple","Single file",value = FALSE),
                                          uiOutput("mult_files"),
                                          uiOutput("sing_file"),
                                          actionButton("disp_distr","Show distributions"),
                                          plotOutput("distr_plot"),
                                          plotOutput("distr_stade")
                     ),
                     tabPanel("Weight fitting",
                              fileInput("weight_data","Choose weight data to be fitted",accept = c("text/csv")),
                              div(style="display:inline-block",selectInput("method_we","Select fitting formula",choices = c("Logistic"="verhulst","Gompertz"="gompertz","Empiric"="empirique","Log polynomial"="log_poly","Double sigmoid"="double_sig"))),
                              div(style="display:inline-block",formula_tabs), ## "Contois"="contois",,"Noyau"="seed",
                              conditionalPanel("input.method_we=='verhulst'",textInput("par1_sig","Enter value of a",value =0.1),
                                               textInput("par2_sig","Enter value of b",value = 100),
                                               textInput("par3_sig","Enter value of c",value = 1)),
                              conditionalPanel("input.method_we=='gompertz'",textInput("par1_sig","Enter value of a",value =0.065),
                                               textInput("par2_sig","Enter value of b",value = 114.39),
                                               textInput("par3_sig","Enter value of c",value = 0.52)),
                              conditionalPanel("input.method_we=='empirique'",textInput("par1_sig","Enter value of a",value =5.38),
                                               textInput("par2_sig","Enter value of b",value = 8),
                                               textInput("par3_sig","Enter value of c",value = 7)),
                              conditionalPanel("input.method_we=='double_sig'",textInput("par1_sig","Enter value of a",value = 48),
                                               textInput("par2_sig","Enter value of b",value = 0.144),
                                               textInput("par3_sig","Enter value of c",value = 35),
                                               textInput("par4_sig","Enter value of d",value = 0.4),
                                               textInput("par5_sig","Enter value of e",value = 48),
                                               textInput("par6_sig","Enter value of f",value = 0.042),
                                               textInput("par7_sig","Enter value of g",value = 90)),
                              actionButton("fit_op","Fit"),
                              plotOutput("fitplot")
                     ),
                     tabPanel("mRNA fitting and calculation",
                              textInput("ksmin","Value of ksmin",value =3*4*3*3.6*24),
                              selectInput("fit_mrna","Select fitting formula",choices=c("3rd degree polynomial"="3_deg","6th degree polynomial"="6_deg","3rd degree logarithmic polynomial"="3_deg_log")),
                              actionButton("run_loop","Run calculation"),
                              disabled(downloadButton("downFile","Save results"))
                     ),
                     tabPanel("Results",id="tabRes",
                              uiOutput("select_res"),
                              plotOutput("fit_prot_plot")
                     )
                     ))
)

server.r

library(shiny)
library(shinythemes)
library(shinyjs)
library(ggplot2)
library(grid)
library(egg)

# source("input.r")
source("functions.r")

function(input, output, session) {
  js$disableTab("tabRes")
  fit_op<-reactiveValues(data=NULL)
  run_calc<-reactiveValues(data=NULL)
  en_but<-reactiveValues(enable=FALSE)
  theme<<-theme(panel.background = element_blank(),panel.border=element_rect(fill=NA),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),strip.background=element_blank(),axis.text.x=element_text(colour="black"),axis.text.y=element_text(colour="black"),axis.ticks=element_line(colour="black"),plot.margin=unit(c(1,1,1,1),"line"))

  output$mult_files<-renderUI({
    if (!input$multiple){
      tagList(fileInput("prot_file","Choose protein file"),
              fileInput("mrna_file","Choose transcript file"))
    }
  })

  output$sing_file<-renderUI({
    if (input$multiple){
      tagList(textInput("protein_tab","Name of protein tab",value = "Proteines"),
              textInput("rna_tab","Name of mRNA tab",value = "Transcrits"),
              fileInput("data_file","Choose xls/xlsx file",accept=c(".xls",".xlsx")))
    }
  })
  observeEvent(input$method_we, {
    # updateTabsetPanel(session, "params", selected = input$method_we)
    updateTabsetPanel(session,"formulas",selected = input$method_we)
  })
  observe({
    if(!is.null(input$data_file)){
      inFile<-input$data_file
      list_data<-loadData(inFile$datapath,input$rna_tab,input$protein_tab,poids=F)
      mrna_data<-list_data$mrna
      prot_data<-list_data$prot
      test_list<-list_data$parse
      test_list<<-sample(test_list,3)
      clean_mrna_data<<-mrna_data[,-which(is.na(as.numeric(as.character(colnames(mrna_data)))))]
      clean_prot_data<<-prot_data[,-which(is.na(as.numeric(as.character(colnames(prot_data)))))]
    }
  }) 
  observe({
    if((!is.null(input$prot_file)) & (!is.null(input$mrna_file))){
      protFile<-input$prot_file
      mrnaFile<-input$mrna_file
      prot_data<-loadData(protFile$datapath,"","",poids=F)
      mrna_data<-loadData(mrnaFile$datapath,"","",poids=F)
      clean_mrna_data<<-mrna_data[,-which(is.na(as.numeric(as.character(colnames(mrna_data)))))]
      clean_prot_data<<-prot_data[,-which(is.na(as.numeric(as.character(colnames(prot_data)))))]

      total_data<-merge(mrna_data,prot_data)
      lista<-vector("list",nrow(mrna_data))
      for (i in seq(1,nrow(total_data))){
        lista[[i]]<-list("Protein_ID"=total_data[i,"Protein"],"Transcrit_ID"=total_data[i,"Transcrit"],"Transcrit_val"=as.matrix(total_data[i,3:29]),"Protein_val"=as.matrix(total_data[i,30:ncol(total_data)]),"DPA"=t)

      }
      # test_list<<-lista
      test_list<<-sample(lista,3)
    }
  })    
  observeEvent(input$disp_distr,{
    print("Plotting...")
    output$distr_plot<-renderPlot({print(combineGraphs(clean_mrna_data,clean_prot_data,"",moyenne = T))})
    print("Finished")
  })

  # parList<-reactiveValues()
  # observe({
  #   for (i in reactiveValuesToList(input)){
  #   print(i)
  #   if (grepl("par[1-9]+_sig",i,perl = T)){
  #     newlist[[input[[i]]]]<-input[[i]]
  #   }
  # }
  # # })

  parList<-reactive({
    x<-reactiveValuesToList(input)
    x_ind<-grep("par[1-9]+",names(x),perl = T)
    newlist<-vector("list",length(x_ind))
    names(newlist)<-names(x[x_ind])
    for (el in names(newlist)){
      newlist[[el]]<-as.numeric(as.character(input[[el]]))
    }
    names(newlist)<-gsub("_sig","",names(newlist))
    newlist<-newlist[order(names(newlist))]
    newlist
  })
  observeEvent(input$fit_op,{
    browser()
    print(parList())
    inFile<-input$weight_data
    days_kiwi<-rep(c(0,13,26,39,55,76,118,179,222), each = 3)
    poids_data<-loadData(inFile$datapath,"","",poids=T)
    print("Fitting...")
    tryCatch({
      coefs_poids<<-fitPoids_v2(poids_data[,1],poids_data[,2],input$method_we,parList())
    },
    warning = function(warn){
      showNotification(paste0(warn), type = 'warning')
    },
    error = function(err){
      showNotification(paste0(err), type = 'err')
    })
    print(coefs_poids$coefs)
    val_mu<-mu(c(poids_data$DPA),input$method_we,coefs_poids$coefs,coefs_poids$formula,dpa_analyse = NULL)
    data_mu<-data.frame("DPA"=c(poids_data$DPA),"Mu"=val_mu)
    g_mu<<-ggplot(data_mu,aes(x=DPA,y=Mu))+geom_line()+theme+xlab("DPA")+ylab("Growth rate (days^-1)")
    fit_op$state<-TRUE
    print("Finished!!")
    output$fitplot<-renderPlot({
      req((fit_op$state)==TRUE,exists("coefs_poids"))
      ggarrange(coefs_poids$graph,g_mu,ncol=2)
    })
  })
  observeEvent(input$run_loop,{
    if (input$fit_mrna!=""){
      ksmin=as.numeric(as.character(input$ksmin))
      score=0
      cont<-0
      poids_coef<<-coefs_poids$coefs
      formula_poids<<-coefs_poids$formula
      mess<-showNotification(paste("Running..."),duration = NULL,type = "message")
      for (el in test_list){
        tryCatch({
          run_calc$run<-TRUE
          cont<-cont+1
          print(cont)
          norm_data<-normaMean(el$Protein_val,el$Transcrit_val,ksmin)
          fittedmrna<<-fit_testRNA(el$DPA,norm_data$mrna,"3_deg")
          par_k<-solgss_Borne(el$DPA,as.vector(norm_data$prot),as.numeric(norm_data$ks),score)
          par_k[["plot_fit_prot"]]<-plotFitProt(el$DPA,as.vector(norm_data$prot),par_k$prot_fit)
          X<-matrice_sens(el$DPA,par_k[["solK"]][,1])
          diff<-(par_k[["error"]][["errg"]][1]*norm(as.vector(norm_data$prot),"2"))^2
          par_k[["corr_matrix"]]<-matrice_corr(X,length(norm_data$prot),diff)
          if (!is.null(par_k)){
            test_list[[cont]]$SOL<-par_k
            # write.csv(test_list[[cont]][["SOL"]][["solK"]],paste("solK/",paste(test_list[[cont]][["Transcrit_ID"]],"_Sol_ks_kd.csv"),sep = ""))
          }
        },error=function(e){showNotification(paste0("Protein fitting not achieved for ",el$Transcrit_ID,sep=" "),type = "error",duration = NULL)})

      }
      valid_res<<-Filter(function(x) {length(x) > 5}, test_list)
      print(valid_res[[1]])
      mess<-showNotification(paste("Finished!!"),duration = NULL,type = "message")
      en_but$enable<-TRUE

    }
  })
  output$downFile<-downloadHandler(
    filename = function(){
      paste("results_KsKd-",Sys.Date(),".zip",sep="")
    },
    content = function(file){
      owd <- setwd(tempdir())
      on.exit(setwd(owd))
      files <- NULL;
      for (res in valid_res){
        fileName<-paste(res[["Transcrit_ID"]],"_Sol_ks_kd.csv",sep = "")
        write.csv(res[["SOL"]][["solK"]],fileName)
        files<-c(files,fileName)
      }
      zip(zipfile = file,files = files)
      if(file.exists(paste0(file, ".zip"))) {file.rename(paste0(file, ".zip"), file)}
    },contentType = "application/zip"

  )
  observe({
    if (en_but$enable){
      enable("downFile")
    }
  })
}

I recently started using Shiny, so any help would be extremely appreciated. Thanks in advance!

Answer 1

Welcome to SO.

You've identified the problem yourself: "...are all named parN_sig". That means you don't have several inputs, you only have one. So you always get the value of (say) input$par2_sig from the first conditional panel regardless of which panel you're trying to access.

You have two options:

1. Provide unique names for every textInput. That will be a pain. Or...
2. Use modules. They take a bit of getting used to, but are worth the effrt in the end.

If you set the module up correctly, you'll be able to use the same module for each conditional panel, even though they have different numbers of textinputs.

See this page for help on creating your first module.