Ajout d'un autre tabPanel pour afficher les données

server.R

-# Shiny app allowing: plot and parameters for microbial growth dataset
-# Marc Garel, Severine Martini, Christian Tamburini
-### October 2017
-
-
-library(shiny)
-
-shinyServer(function(input, output) {
-  output$contents <- renderTable({
-    
-    inFile <- input$file1
-    
-    if (is.null(inFile))
-      return(NULL)
-    
-    dd<-read.csv(inFile$datapath, header=input$header, sep=input$sep, 
-             quote=input$quote)
-    do<-reactiveValues(data=dd)
-
-        #calcul coef pour affichage dans en dessous du graph
-    x=rep(dd[,1],ncol(dd)-1)
-    y=unlist(dd[,2:ncol(dd)])
-    crssce=data.frame(y,x)
-    fit=nls(y~SSlogis(x,Asym,xmid,scal),crssce)
-    param=summary(fit)$parameters
-    mu=round(1/param[3,1],digits=3)
-    sdmu=round((1/summary(fit)$parameters[3,1])-(1/(summary(fit)$parameters[3,1]+summary(fit)$parameters[3,2])), digits=3)
-    asym=round(param[1,1],digits=3)
-    sdasym=round(summary(fit)$parameters[1,2], digits=3)
-    #####Le graph
-    
-    output$plot <- renderPlot({
-      
-      
-      ##############
-      x=rep(dd[,1],ncol(dd)-1)
-      y=unlist(dd[,2:ncol(dd)])
-      crssce=data.frame(y,x)
-      require("quantreg")
-      # limit axes extended
-      maxx=max(x,na.rm=T)+(max(x,na.rm=T)/4)
-      maxy=max(y,na.rm=T)+(max(y,na.rm=T)/4)
-      w0=seq(0,maxx)
-      # modlog2=nls(x ~ SSlogis(y,Asym,xmid,scal),crssce)
-      # modlog=nls(y ~ SSlogis(x,Asym,xmid,scal),crssce)
-      coef=getInitial(y~SSlogis(x,asym,xmid,scal),data=cbind.data.frame(x,y))
-      mu=1/coef[3]
-      # output plot
-      plot(x,y)
-      points(x,y,xlim=c(0,maxx),ylim=c(0,maxy),xlab="temps(h)",ylab="DO600nm",las=1,pch=22,bg=1)
-      lines(w0,SSlogis(w0,coef[1],coef[2],coef[3]),lwd=1.5)
-      q1b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.25,data=crssce)
-      q3b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.75,data=crssce)
-      q05b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.025,data=crssce)
-      q95b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.975,data=crssce)
-      lines(w0, predict(q1b, newdata=list(x=w0)), col="blue",lty=2)
-      lines(w0, predict(q3b, newdata=list(x=w0)), col="blue",lty=2)
-      lines(w0, predict(q05b, newdata=list(x=w0)), col="blue",lty=3)
-      lines(w0, predict(q95b, newdata=list(x=w0)), col="blue",lty=3)
-
-      observeEvent(input$clicks, {print(as.numeric(do$data))})
-     
-    })
-     output$ex_out <- renderPrint({return(c(mu,sdmu,asym,sdasym))})
-
-     })
-      output$txtout <- renderText({
-    
-    paste("Martini, S., B. Al Ali, M. Garel, and others. 2013. Effects of Hydrostatic Pressure on Growth and Luminescence of a Moderately-Piezophilic Luminous Bacteria Photobacterium phosphoreum ANT-2200 A. Driks [ed.]. PLoS One 8: e66580. doi:10.1371/journal.pone.0066580")
-  })
-
-})
-
-# shinyServer(function(input, output, session) {
-#output$main_plot <- renderPlot({
-#    plot(dd$H,dd$A, type=input$plotType)
-
-#   
-#   
-#   output$table <- DT::renderDataTable({
-#     DT::datatable(cars)
-#   })
+# Shiny app allowing: plot and parameters for microbial growth dataset
+# Marc Garel, Severine Martini, Christian Tamburini
+### October 2017
+
+
+library(shiny)
+
+shinyServer(function(input, output) {
+  output$contents <- renderTable({
+    
+    inFile <- input$file1
+    
+    if (is.null(inFile))
+      return(NULL)
+    
+    dd<-read.csv(inFile$datapath, header=input$header, sep=input$sep, 
+             quote=input$quote)
+    do<-reactiveValues(data=dd)
+
+   #calcul coef pour affichage dans en dessous du graph
+    x=rep(dd[,1],ncol(dd)-1)
+    y=unlist(dd[,2:ncol(dd)])
+    crssce=data.frame(y,x)
+    fit=nls(y~SSlogis(x,Asym,xmid,scal),crssce)
+    param=summary(fit)$parameters
+    mu=round(1/param[3,1],digits=3)
+    sdmu=round((1/summary(fit)$parameters[3,1])-(1/(summary(fit)$parameters[3,1]+summary(fit)$parameters[3,2])), digits=3)
+    asym=round(param[1,1],digits=3)
+    sdasym=round(summary(fit)$parameters[1,2], digits=3)
+    #####Le graph
+    
+    
+    
+    output$plot <- renderPlot({
+      
+      
+      ##############
+      x=rep(dd[,1],ncol(dd)-1)
+      y=unlist(dd[,2:ncol(dd)])
+      crssce=data.frame(y,x)
+      require("quantreg")
+      # limit axes extended
+      maxx=max(x,na.rm=T)+(max(x,na.rm=T)/4)
+      maxy=max(y,na.rm=T)+(max(y,na.rm=T)/4)
+      w0=seq(0,maxx)
+      # modlog2=nls(x ~ SSlogis(y,Asym,xmid,scal),crssce)
+      # modlog=nls(y ~ SSlogis(x,Asym,xmid,scal),crssce)
+      coef=getInitial(y~SSlogis(x,asym,xmid,scal),data=cbind.data.frame(x,y))
+      mu=1/coef[3]
+      # output plot
+      plot(x,y)
+      points(x,y,xlim=c(0,maxx),ylim=c(0,maxy),xlab="temps(h)",ylab="DO600nm",las=1,pch=22,bg=1)
+      lines(w0,SSlogis(w0,coef[1],coef[2],coef[3]),lwd=1.5)
+      q1b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.25,data=crssce)
+      q3b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.75,data=crssce)
+      q05b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.025,data=crssce)
+      q95b=nlrq(y~SSlogis(x,K, xmid, r),tau=0.975,data=crssce)
+      lines(w0, predict(q1b, newdata=list(x=w0)), col="blue",lty=2)
+      lines(w0, predict(q3b, newdata=list(x=w0)), col="blue",lty=2)
+      lines(w0, predict(q05b, newdata=list(x=w0)), col="blue",lty=3)
+      lines(w0, predict(q95b, newdata=list(x=w0)), col="blue",lty=3)
+
+      observeEvent(input$clicks, {print(as.numeric(do$data))})
+     
+    })
+    output$ex_out <- renderPrint({return(c(mu,sdmu,asym,sdasym))})
+    output$ex_out2 <- renderPrint({return(dd)})
+
+     })
+      output$txtout <- renderText({
+    
+    paste("Martini, S., B. Al Ali, M. Garel, and others. 2013. Effects of Hydrostatic Pressure on Growth and Luminescence of a Moderately-Piezophilic Luminous Bacteria Photobacterium phosphoreum ANT-2200 A. Driks [ed.]. PLoS One 8: e66580. doi:10.1371/journal.pone.0066580")
+  })
+
+})
+
+# shinyServer(function(input, output, session) {
+#output$main_plot <- renderPlot({
+#    plot(dd$H,dd$A, type=input$plotType)
+
+#   
+#   
+#   output$table <- DT::renderDataTable({
+#     DT::datatable(cars)
+#   })
 # })
\ No newline at end of file

ui.R

@@ -35,6 +35,7 @@ titlePanel("Upload file"),
       helpText('Logistic equation $$x(t) =r.x_0.(1-\\frac{x_0}K)$$'),
       tabsetPanel(
       tabPanel("Details",tableOutput('contents'),  helpText('You have to format data with tab separartor and dot for decimal. Remove all space in the header from your dataset. Replace it by "_"'),helpText('In your data set there are two arrays, time and cells density (Optic density, Cells number, Biomass ....) ')),
+      tabPanel("Data",verbatimTextOutput('ex_out2')),
       tabPanel("Plot",plotOutput('plot'), verbatimTextOutput('ex_out'))
       )
     )