@@ -162,16 +162,19 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

       # }

       if(loadpage_input()$DDA_DIA == "TMT"){

-        

-        dataProcessPlotsTMT(preprocess_data(),

+        print("in tmt")

+        print(input$type1)

+        plot <- dataProcessPlotsTMT(preprocess_data(),

                             type=input$type1,

                             ylimUp = FALSE,

                             ylimDown = FALSE,

                             which.Protein = protein,

                             originalPlot = TRUE,

                             summaryPlot = input$summ,

-                            address = file

-        )

+                            address = file,

+                            isPlotly = TRUE

+        )[[1]]

+        return(plot)

       } else if (loadpage_input()$BIO == "PTM"){

@@ -371,7 +374,7 @@ qcServer <- function(input, output, session,parent_session, loadpage_input,get_d

     ns<- session$ns

     # TMT and PTM plotly plots are still under development

-    if ((loadpage_input()$DDA_DIA == "TMT") || (loadpage_input()$BIO == "PTM")) {

+    if ((loadpage_input()$DDA_DIA == "TMT--") || (loadpage_input()$BIO == "PTM")) {

       output$theplot = renderPlot(theplot())

       op <- plotOutput(ns("theplot"))

     } else {