ui.R

library("shiny")
library("plotly")
library("XLConnectJars")
library("XLConnect")


options(shiny.sanitize.errors = FALSE, shiny.minified = TRUE)

fluidPage(
  
  id = "Q2_form",
  
  shinyjs::useShinyjs(),
  
  tags$h1("Q2 Analyser"),
  tags$br(),
  textOutput("catch_notice"),
  uiOutput("data_download"),
  tags$br(),
    
  
  
  tabsetPanel(id = "tabs",
    tabPanel("Q2 Data", value = "Q2_data_tab",
      fluidRow(
        column(3,
          tags$h1("Upload Q2 Data File"),
          fileInput("xlsInput", "", accept = c(".xls",".xlsx")),
          textOutput("data_notice"),  
          uiOutput("data_blanks")
        )
      ),
      
      fluidRow(
        tableOutput("Q2_Data")
        )
      ),
    
    
    
    tabPanel("Q2 Metadata", value = "Q2_metadata_tab",
      fluidRow(
        column(3,
          tags$h1("Metadata File"),
          downloadButton("downloadTemplate", "Download Metadata Template (.xlsx)"),
          fileInput("metadata","", accept = c(".xls",".xlsx")),
          textOutput("meta_notice"),
          tags$h1("Q2 Conditions"),
          textInput("sitePressure","Site Pressure (kPa)"),
          textInput("altitude","Altitude (m)"),
          checkboxInput("is_MSLP", "Has the pressure been normalised to sea level (Mean Sea Level Pressure)?", value = FALSE),
          textInput("tubeVol","Tube Vol (mL)"),
          textInput("temperature","Temperature (C)")
        ),
        column(6,
          tableOutput("Q2_Meta")
        )
      )
    ),
      
    
    
    navbarMenu("Analysis",
      tabPanel("Fluorescence", value = "Q2_fluoro_tab",
        
        textOutput("fluoro_notice"),
        plotlyOutput("fluoro"),
        uiOutput("fluoro_slider"),
        fluidRow(
          column(1,
            uiOutput("fluoro_start_spot")
          ),
          column(1,
            uiOutput("fluoro_end_spot")
          )
        ),
        fluidRow(
          column(2,
            textOutput("fluro_duration")
          )
        )
      ),
      
      
     tabPanel("Respiration", value = "Q2_resp_tab",
        
      fluidPage(
        textOutput("respiration_notice"),
          column(1,
            tableOutput("respiration")
          ),
          column(5, offset=6,
                 tableOutput("Resp_Meta")
          ),
          column(5,offset=6,
                 plotlyOutput("Resp_Area"),
                 tags$br(),
                 plotlyOutput("Resp_Fresh_Mass"),
                 tags$br(),
                 plotlyOutput("Resp_Dry_Mass")
          )
        )
      )
    ),
    
    
    
    tabPanel("Help", value = "Q2_help_tab",
            tags$h2("Help and instructions are actively in development. In the meantime, contact Darren Cullerne for help!"),
            tags$a(href="mailto:darren.cullerne@anu.edu.au", "darren.cullerne@anu.edu.au"),
            textOutput("temp1"),
            tags$br(),
            tags$br(),
            tags$h2("Q2 Analyser - Instructions"),
            tags$br(),
            includeHTML("www/Q2_analyser_help_documentation.html")
    )
  )
)