inst/app/server.R

In thierrycnam/masan: masan uses bioconductor to analyze microarray data

function(input, output, session) {

  ## Outputs
  list_1 <- callModule(masanData, "masan", stringsAsFactors=FALSE)

  # df_react_1 <- callModule(masanData, "masan",
                         # stringsAsFactors = FALSE)
  df_react_1 <- reactive({
    df_1 <- list_1$df_1
    df_1()
  })

  df_react_2 <- reactive({
    df_2 <- list_1$df_path
    df_2()
  })

  react_affy_raw <- reactive({
    affy_raw <- list_1$affy_raw
    affy_raw()
  })

  react_expr_raw <- reactive({
    expr_raw <- list_1$expr_raw
    expr_raw()[1:5,1:5]
  })


  output$table_1 <- renderDataTable({
    df_react_1()
  })

  output$table_2 <- renderDataTable({
    df_react_2()
  })

  output$dt_expr_raw <- renderDataTable({
    as.data.frame(react_expr_raw()[1:5, 1:5])
  })

  # Render Prints
  output$render_affy_raw <- renderPrint({
    head(react_affy_raw())
  })

  output$render_sel_input_ui_1 <- renderPrint({
    input$sel_input_ui_1
  })

  output$render_sel_input_ui_2 <- renderPrint({
    input$sel_input_ui_2
  })

  # Combine the selected variables into a new data frame
  selectedData <- reactive({
    iris[, c(input$xcol, input$ycol)]
  })

  clusters <- reactive({
    kmeans(selectedData(), input$clusters)
  })

  output$plot1 <- renderPlot({
    palette(c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3",
              "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"))

    par(mar = c(5.1, 4.1, 0, 1))
    plot(selectedData(),
         col = clusters()$cluster,
         pch = 20, cex = 3)
    points(clusters()$centers, pch = 4, cex = 4, lwd = 4)
  })

  output$select_input_ui_1 <- renderUI({
    validate(
      need(df_react_1(), message="df_1() needed for renderUI 1")
    )
    list_items <- as.list(colnames(df_react_1()))
    selectInput("sel_input_ui_1", label=h6("Color"),
                choices=list_items)
  })

  output$select_input_ui_2 <- renderUI({
    validate(
      need(df_react_1(), message="df_1() needed for renderUI 1")
    )
    list_items <- as.list(colnames(df_react_1()))
    selectInput("sel_input_ui_2", label=h6("Shape"),
                choices=list_items)
  })
}