inst/app/tools/bioCancer/Mutation.R

In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

output$MutDataTable <- DT::renderDataTable({
  ## check if GenProf is mutation

  if (length(grep("mutation", input$GenProfID))==0){

    dat <- as.data.frame("Please select mutations from Genetic Profiles")

  }else{
    GeneList <- whichGeneList(input$GeneListID)

    ##### Get Mutation Data for selected Case and Genetic Profile
    if(length(GeneList)>500){

      shiny::withProgress(message = 'loading Mega Mutation Data from cgdsr server...', value = 1, {

        dat <- getMegaProfData(GeneList,input$GenProfID,input$CasesID, Class="MutData")
      })

    } else if (inherits(try(dat <- cgdsr::getMutationData(cgds,input$CasesID, input$GenProfID, GeneList), silent=FALSE),"try-error")){

      dat <- as.data.frame("There are some Gene Symbols not supported by cbioportal.
                           Or the gene list is empty.
                           Or bioCancer is not connected to cgdsr server (check connection).")
    }else{
      shiny::withProgress(message = 'loading Mutation Data from cgdsr server...', value = 1, {

        dat <- cgdsr::getMutationData(cgds,input$CasesID, input$GenProfID, GeneList)


        if(dim(dat)[1]==0){
          ## avoide error when GeneList is empty
          ## Error..No.cancer.study..cancer_study_id...or.genetic.profile..genetic_profile_id..or.case.list.or..case_list..case.set..case_set_id..provid
          dat <- as.data.frame("Gene List is empty.
                               Or The Gene Symbols are not supported by cbioportal.
                               Copy and paste genes from text file (Gene/line) or use gene list from examples.")
        }else{
          req(input$Mut_varsID)
          # dat <- cgdsr::getMutationData(cgds,input$CasesID, input$GenProfID, GeneList)
          ## change rownames in the first column
          dat <- as.data.frame(dat %>% tibble::rownames_to_column("Patients"))
          dat <- dat[input$Mut_varsID]
          r_data[['MutData']] <- dat
        }
      })
    }
  }
  displayTable(dat)%>% DT::formatStyle(names(dat),
                                       color = DT::styleEqual("Gene List is empty. copy and paste genes from text file (Gene/line) or use gene list from examples.",
                                                              'red'))#, backgroundColor = 'white', fontWeight = 'bold'
})


output$dl_MutData_tab <- shiny::downloadHandler(
  filename = function() { paste0("MutData_tab.csv") },
  content = function(file) {
    #data_filter <- if (input$show_filter) input$data_filter else ""
    get_data(r_data$MutData[input$MutDataTable_rows_all,], vars = input$Mut_varsID,
            rows = NULL, na.rm = FALSE) %>%
      write.csv(file, row.names = FALSE)
  }
)


observeEvent(input$MutationHelp_report, {

  cmd <- paste0("```{r fig.width=10.46, fig.height=5.54, dpi =72}\n",
                paste0(" get_data(MutData[input$MutDataTable_rows_all,], vars = input$Mut_varsID,
                       na.rm = FALSE)"),
                "\n",
                "\n```\n"
  )
  update_report_fun(cmd)
})