# This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#

library(shiny)
library(shinyjs) #http://deanattali.com/shinyjs/
library(plotly)

shinyUI(fluidPage(
  useShinyjs(),
  # Include shinyjs
  
  # Application title
  title = "Timecourse Inspector",
  
  sidebarLayout(
    sidebarPanel(
      #Selector for file upload
      fileInput(
        'inFileLoadNuc',
        'Select data file (e.g. tCoursesSelected.csv) and press "Load Data"',
        accept = c('text/csv', 'text/comma-separated-values,text/plain')
      ),
      actionButton("inButLoadNuc", "Load Data"),
      actionButton("butReset", "Reset file input"),
      actionButton('inDataGen1', 'Generate artificial dataset'),

      tags$hr(),
      checkboxInput('chBtrackUni', 'Track Label unique across entire dataset', FALSE),
      uiOutput('varSelSite'),
      uiOutput('varSelTrackLabel'),
      uiOutput('varSelGroup'),
      uiOutput('varSelTime'),
      uiOutput('varSelMeas1'),
      radioButtons(
        'inSelMath',
        'Math operation 1st and 2nd meas.:',
        c(
          'None' = '',
          'Divide' = " / ",
          'Sum' = " + ",
          'Multiply' = " * ",
          'Subtract' = ' - ',
          '1 / X' = '1 / '
        )
      ),
      uiOutput('varSelMeas2'),
      
      tags$hr(),
      checkboxInput('chBtimeTrim', 'Trim x-axis', FALSE),
      uiOutput('uiSlTimeTrim'),
      tags$hr(),
      checkboxInput('chBnorm', 'Normalization', FALSE),
      uiOutput('uiChBnorm'),
      uiOutput('uiSlNorm'),
      uiOutput('uiChBnormRobust'),
      uiOutput('uiChBnormGroup'),
      tags$hr(),
      checkboxInput('chBoutliers', 'Remove outliers', FALSE),
      uiOutput('uiSlOutliers'),
      uiOutput("uiTxtOutliers"),
      downloadButton('downloadDataClean', 'Download mod\'d data')
    ),
    
    mainPanel(tabsetPanel(
      tabPanel(
        "Time courses",
        h4(
          "Plot time series"
        ),
  
        br(),
        checkboxInput('chBhighlightTraj', 'Highlight trajectories?', FALSE),
        uiOutput('varSelHighlight'),
        br(),
        fluidRow(
          column(
            4,
            numericInput(
              'inPlotTrajFacetNcol',
              '#Columns:',
              value = 4,
              min = 1,
              width = '100px',
              step = 1
            ),
            checkboxInput('chBplotTrajInt', 'Interactive Plot?'),
            actionButton('butPlotTraj', 'Plot!')
          ),
          column(
            4,
            sliderInput('sliPlotTrajSkip', 'Plot every n-th point:', min = 1, max = 10, value = 1, step = 1)
          ),
          column(
            4,
            numericInput(
              'inPlotTrajWidth',
              'Width [%]:',
              value = 100,
              min = 10,
              max = 100,
              width = '100px',
              step = 10
            ),
            numericInput(
              'inPlotTrajHeight',
              'Height [px]:',
              value = 800,
              min = 100,
              width = '100px',
              step = 50
            )
          )
        ),
        uiOutput('uiPlotTraj'),
        downPlotUI('downPlotTraj', "Download PDF")
      ),
      
      tabPanel(
        "Box-plots",
        tabBoxPlotUI('tabBoxPlot')
      ),
      

      # scatter plot
      tabPanel(
        'Scatter',
        tabScatterPlotUI('tabScatter')
      ),
      
      tabPanel(
        'Hierarchical',
        br(),
        fluidRow(
          column(4,
            selectInput(
              "selectPlotHierLinkage",
              label = ("Select linkage method:"),
              choices = list(
                "Ward" = 1,
                "Ward D2" = 2,
                "Single" = 3,
                "Complete" = 4,
                "Average" = 5,
                "McQuitty" = 6,
                "Centroid" = 7
              ),
              selected = 2
            ),
            selectInput(
              "selectPlotHierDiss",
              label = ("Select type of dissimilarity measure:"),
              choices = list("Euclidean" = 1,
                             "Maximum" = 2,
                             "Manhattan" = 3,
                             "Canberra" = 4,
                             "Binary" = 5,
                             "Minkowski" = 6),
              selected = 1
            )
          ),
          column(4,
                 sliderInput(
                   'inPlotHierNclust',
                   '#dendrogram branches to colour',
                   min = 1,
                   max = 20,
                   value = 1,
                   step = 1,
                   ticks = TRUE,
                   round = TRUE
                 ),
                 checkboxInput('chBPlotHierClSel', 'Manually select clusters to display'),
                 uiOutput('uiPlotHierClSel'),
                 #downCellClUI('downDataHier', "Download Data")
                 downloadButton('downCellCl', 'Download CSV with cell IDs and cluster no.')
          )
        ),
        br(),
        #checkboxInput('inPlotHierSparInteractive', 'Interactive Plot?',  value = FALSE),
        
        tabsetPanel(
          tabPanel('Heat-map',
                   fluidRow(
                     column(3,
                            checkboxInput('selectPlotHierDend', 'Plot dendrogram and re-order samples', TRUE),
                            selectInput(
                              "selectPlotHierPalette",
                              label = "Select colour palette:",
                              choices = l.col.pal,
                              selected = 'Spectral'
                            ),
                            checkboxInput('inPlotHierRevPalette', 'Reverse colour palette', TRUE),
                            checkboxInput('selectPlotHierKey', 'Plot colour key', TRUE)
                     ),
                     column(3,
                            sliderInput(
                              'inPlotHierNAcolor',
                              'Shade of grey for NA values (0 - black, 1 - white)',
                              min = 0,
                              max = 1,
                              value = 0.8,
                              step = .1,
                              ticks = TRUE
                            ),
                            numericInput('inPlotHierHeatMapHeight', 
                                         'Display plot height [px]', 
                                         value = 600, 
                                         min = 100,
                                         step = 100)
                     ),
                     column(6,
                            h4('Classic hierarchical clustering')
                     )
                   ),
                   
                   fluidRow(
                     column(
                       3,
                       numericInput(
                         'inPlotHierMarginX',
                         'Margin below x-axis',
                         5,
                         min = 1,
                         width = 100
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierMarginY',
                         'Margin right of y-axis',
                         20,
                         min = 1,
                         width = 100
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierFontX',
                         'Font size row labels',
                         1,
                         min = 0,
                         width = 100,
                         step = 0.1
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierFontY',
                         'Font size column labels',
                         1,
                         min = 0,
                         width = 100,
                         step = 0.1
                       )
                     )
                   ),
                   br(),
                   
                   downPlotUI('downPlotHier', "Download PDF"),
                   actionButton('butPlotHierHeatMap', 'Plot!'),
                   plotOutput('outPlotHier')
          ),
          # tabPanel('Heat-map int.',
          #          helpText("Choose your settings 2")),
          tabPanel('Time-courses',
                   downPlotUI('downPlotHierTraj', "Download PDF"),
                   actionButton('butPlotHierTraj', 'Plot!'),
                   plotOutput('outPlotHierTraj')),
          tabPanel('Cluster dist.',
                   downPlotUI('downPlotHierClDist', "Download PDF"),
                   actionButton('butPlotHierClDist', 'Plot!'),
                   plotOutput('outPlotHierClDist'))
        )
      ),
      
      
      tabPanel(
        'Hier. Sparse',
        br(),
        fluidRow(
          column(
            6,
            selectInput(
              "selectPlotHierSparLinkage",
              label = ("Select linkage method:"),
              choices = list(
                "Average" = 1,
                "Complete" = 2,
                "Single" = 3,
                "Centroid" = 4
              ),
              selected = 1
            ),
            selectInput(
              "selectPlotHierSparDiss",
              label = ("Select type of dissimilarity measure:"),
              choices = list("Squared Distance" = 1,
                             "Absolute Value" = 2),
              selected = 1
            ),
            sliderInput(
              'inPlotHierSparNclust',
              '#dendrogram branches to colour',
              min = 1,
              max = 30,
              value = 1,
              step = 1,
              ticks = TRUE,
              round = TRUE
            )
          ),
          
          column(
            6,
            checkboxInput('inHierSparAdv',
                          'Advanced options',
                          FALSE),
            uiOutput(
              'uiPlotHierSparNperms'
            ),
            uiOutput(
              'uiPlotHierSparNiter'
            ),
            checkboxInput('chBPlotHierSparClSel', 'Manually select clusters to display'),
            uiOutput('uiPlotHierSparClSel'),
            downloadButton('downCellClSpar', 'Download CSV with cell IDs and cluster no.')
          )
        ),
        
        
        br(),
        #checkboxInput('inPlotHierSparInteractive', 'Interactive Plot?',  value = FALSE),
        
        tabsetPanel(
          tabPanel('Heat-map',
                   fluidRow(
                     column(3,
                            radioButtons(
                              "selectPlotHierSparDend",
                              label = 'Dendrogram',
                              choices = list(
                                'Plot dendrogram; order samples accordingly' = 1,
                                'Don\'t plot dendrogram; retain original ordering' = 2
                              ),
                              selected = 1
                            ),
                            selectInput(
                              "selectPlotHierSparPalette",
                              label = "Select colour palette:",
                              choices = l.col.pal,
                              selected = 'Spectral'
                            ),
                            checkboxInput('inPlotHierSparRevPalette', 'Reverse colour palette', TRUE),
                            checkboxInput('selectPlotHierSparKey', 'Plot colour key', TRUE)
                     ),
                     column(3,
                            sliderInput(
                              'inPlotHierSparNAcolor',
                              'Shade of grey for NA values (0 - black, 1 - white)',
                              min = 0,
                              max = 1,
                              value = 0.8,
                              step = .1,
                              ticks = TRUE
                            )
                     ),
                     column(6,
                            br(),
                            h4(
                              "Sparse hierarchical clustering using ",
                              a("sparcl", href = "https://cran.r-project.org/web/packages/sparcl/")
                            ),
                            p(
                              'Column labels in the heat-map are additionally labeld according to their \"importance\":'
                            ),
                            tags$ol(
                              tags$li("Black - not taken into account"),
                              tags$li("Blue with \"*\" - low importance (weight factor in (0, 0.1]"),
                              tags$li("Green with \"**\" - medium importance (weight factor in (0.1, 0.5]"),
                              tags$li("Red with \"***\" - high importance (weight factor in (0.5, 1.0]")
                            )
                     )
                   ),
                   
                   fluidRow(
                     column(
                       3,
                       numericInput(
                         'inPlotHierSparMarginX',
                         'Margin below x-axis',
                         5,
                         min = 1,
                         width = 100
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierSparMarginY',
                         'Margin right of y-axis',
                         20,
                         min = 1,
                         width = 100
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierSparFontX',
                         'Font size row labels',
                         1,
                         min = 0,
                         width = 100,
                         step = 0.1
                       )
                     ),
                     column(
                       3,
                       numericInput(
                         'inPlotHierSparFontY',
                         'Font size column labels',
                         1,
                         min = 0,
                         width = 100,
                         step = 0.1
                       )
                     )
                   ),
                   br(),
                   
                   
                   downPlotUI('downPlotHierSparHM', "Download PDF"),

                   numericInput('inPlotHierSparHeatMapHeight', 
                                'Display plot height [px]', 
                                value = 600, 
                                min = 100,
                                step = 100),
                   
                   actionButton('butPlotHierSparHeatMap', 'Plot!'),
                   plotOutput('outPlotHierSpar')
          ),
          # tabPanel('Heat-map int.',
          #          helpText("Choose your settings 2")),
          tabPanel('Time-courses',
                   downPlotUI('downPlotHierSparTraj', "Download PDF"),
                   actionButton('butPlotHierSparTraj', 'Plot!'),
                   plotOutput('outPlotHierSparTraj')),
          tabPanel('Cluster dist.',
                   downPlotUI('downPlotHierSparClDist', "Download PDF"),
                   actionButton('butPlotHierSparClDist', 'Plot!'),
                   plotOutput('outPlotHierSparClDist'))
        )
      )
      # 
      # tabPanel(
      #   'Bayesian Cl.',
      #   clustBayUI('TabClustBay'))
      
    ))
  )
))