ui.R

#
# SHINY UI
# ***********************************************
# Define user interface for application
ui <- navbarPage(
  
  # Title on NavBar Header
  title = "ShinyLib - interactive gene fitness analysis",
  
  # Use one of different shiny themes
  theme = shinytheme("cosmo"),
  #shinythemes::themeSelector(),
  
  tabPanel("App",
    
    # Sidebar
    sidebarLayout(
      
      # HERE COME ALL CONTROLS FOR THE SIDEBAR PANEL
      sidebarPanel(width = 5,
        
        # SELECT DATA
        # -------------------
        # select data file
        h4("DATA OPTIONS"),
        
        fluidRow(
          column(width = 6,
            selectInput("UserDataChoice",
              "Choose data:", data_list, 
              selected = data_list[1])
          ),
          column(width = 6,
            uiOutput("UserFilters")
          )
        ),
        
        # SELECT PLOT OPTIONS
        # -------------------
        
        hr(),
        h4("PLOT OPTIONS"),
        fluidRow(
          
          # FACTORIZATION AND ORDERING OPTIONS
          column(width = 4,
            uiOutput("UserXVariable")
          ),
          column(width = 4, 
            uiOutput("UserYVariable")
          ),
          column(width = 4,
            uiOutput("UserCondVariable")
          )
        ),
        
        fluidRow(
          
          # DATA GROUPING OPTIONS
          column(width = 3,
            uiOutput("UserTheme")
          ),
          column(width = 3,
            uiOutput("UserGrouping")
          ),
          column(width = 3,
            uiOutput("UserPlotType")
          ),
          column(width = 3,
            uiOutput("UserLogY")
          )
        ),
        
        # OTHER GRAPHICAL PLOT OPTIONS
        fluidRow(
          
          # PANEL LAYOUT AND PLOT DIMESNIONS
          column(width = 4, 
            selectInput("UserPanelLayout", 
              "Panel layout:", choices = list("automatic", "manual"),
              selected = "automatic")
          ),
          column(width = 2, 
            conditionalPanel(condition = "input.UserPanelLayout == 'manual'",
              numericInput("UserPanelLayoutCols", 
                "Columns:", value = 4)
            )
          ),
          column(width = 2, 
            conditionalPanel(condition = "input.UserPanelLayout == 'manual'",
              numericInput("UserPanelLayoutRows", 
              "Rows:", value = 4)
            )
          ),
          column(width = 2, 
            selectInput("UserPrintHeight",
              "Plot height:", choices = c(1:10*100), selected = 700)
          ),
          column(width = 2, 
            selectInput("UserPrintWidth",
              "Plot width:", choices = c("auto", 1:10*100), selected = "auto")
          )
        ),
        
        hr(),
        fluidRow(
          
          # SELECT GENES OR PROTEINS FROM TREE
          column(width = 6, 
            h4("GENE SELECTION"),
            shinyTree("tree", search = TRUE, checkbox = TRUE)
          ),
          
          # INFO BOX WITH CONTACT AND REFERENCES (EXTERNAL)
          helpbox(width = 6)
          
        )
      ),
      
      
      # MAIN PANEL WITH OUTPUT PLOTS
      # Each tab has individual Download buttons
      column(width = 7,
        wellPanel(
          tabsetPanel(
            tabPanel("DEPLETION / ENRICHMENT", uiOutput("dotplot.ui"),
              downloadButton("UserDownloadDotplot", "Download svg"),
              help_dotplot()
            ),
            tabPanel("HEAT MAP", uiOutput("heatmap.ui"),
              downloadButton("UserDownloadHeat", "Download svg"),
              help_heatmap()
            ),
            tabPanel("FITNESS COMPARISON", uiOutput("fitness.ui"),
              downloadButton("UserDownloadFitness", "Download svg"),
              help_fitness()
            ),
            #tabPanel("CLUSTERING", uiOutput("clustering.ui"),
            #  numericInput("UserNClust", label = "N cluster", value = 4, step = 1)
            #),
            tabPanel("TABLE", uiOutput("table.ui"),
              downloadButton("UserDownloadTable", "Download table")
            )
          )
        )
      )
    )
  ),
  
  # THE ABOUT PAGE
  tabPanel("About", 
    # THE SAME OR A BIT EXTENDED HELP BOX AS IN SIDEBAR
    column(width = 4,
      helpbox(width = 12),
      fundbox(width = 12),
    ),
    column(width = 8,
      methbox(width = 12)
    )
  )

)