inst/shinyApp/ui.R

In ArthurPERE/RNASeqDE:

dashboardPagePlus(
  header = dashboardHeaderPlus(title = "RNA-seq DE"), title = "RNAseqDE",
  sidebar = dashboardSidebar(
    sidebarMenu(
      id = "mnu_MENU",
      menuItem("Load dataset and parameters", tabName = "tab_LOAD", icon = icon("database")),
      menuItem("Result", tabName = "tab_RES", icon = icon("chart-area")),
      menuItem("Analysis", tabName = "tab_ANA", icon = icon("flask"))
    )
  ),
  body = dashboardBody(
    # useShinyalert(),
    useShinyFeedback(),
    useShinyjs(),
    tabItems(

      # load dataset ------------------------------------------------------------
      tabItem(
        "tab_LOAD",
        fluidRow(
          box(
            width = 2, # box with the file input
            title = "Comptage Table",
            TableInput("comptage_table")
          ),
          box(
            width = 2, # box for the parameters files
            title = "parameters files",
            FileInput("param_in", "Select parameters file", accept = c("application/json"))
          ),

          #
          hidden(boxWithId(
            width = 8,
            id = "box_DATASET", title = "Extract of the dataset",
            rHandsontableOutput("comptage_table-table_DATASET")
          )),
          hidden(boxWithId(
            width = 12,
            id = "box_PARAM", title = "Parameters",

            boxParameters("parameters")
          )),
          column(3, offset = 9, hidden(
            downloadBttn("down_PARAM", label = "Download the parameters", style = "bordered", color = "primary"),
            actionBttn("but_DATASET", "Continue", style = "simple", color = "primary")
          ))
        )
      ),

      # Result of the DE --------------------------------------------------------
      tabItem(
        "tab_RES",
        fluidRow(
          box_PlotOutput_ui("normalization", "Normalizations"),
          comparison_BoxOutput_ui("comparison", "Comparisons"),
          box_PlotOutput_ui("heatmap", "Heatmaps"),
          column(3,
            offset = 9,
            downloadBttn("down_RESULT", style = "bordered", color = "primary"),
            actionBttn("but_RES", "Continue", style = "simple", color = "primary")
          )
        )
      ),


      # Analysis of the result --------------------------------------------------

      tabItem(
        "tab_ANA",
        fluidRow(
          # the first box with the tools of analysis and the download button
          box(
            width = 12, title = "Tools for analysis",
            column(12,
              align = "left", style = "display: flex;flex-direction: row;align-items: center;",
              div(style = "width: 90%", checkboxGroupInput("chkgrp_TOOLS", "Choose the tools",
                inline = T,
                choices = c("PCA", "tSNE", "self organizing map" = "SOM", "DBSCAN", "ABOD", "isolation forest" = "ISOFOR")
              )),
              div(style = "width: 10%", downloadBttn("down_ANA", style = "bordered", color = "primary"), offset = 10)
            )
          ),

          tags$style(".nav-tabs-custom {overflow : auto}"),
          tabBox(title = "Tools", id = "tabs_tools", width = 12)
        )
      )
    )
  ),
  footer = dashboardFooter(socialButton(
    url = "https://github.com/ArthurPERE/RNASeqDE/issues",
    type = "github"
  ))
)