ui.R 38.3 KB
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library(shinydashboard)
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if (!require(rNVD3)) {
  install.packages('rNVD3')
  library(rNVD3)
}
if (!require(psych)) {
  install.packages('psych')
  library(psych)
}
if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}
if (!require(vegan)) {
  install.packages('vegan')
  library(vegan)
}
if (!require(dendextend)) {
  install.packages('dendextend')
  library(dendextend)
}
if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}
if (!require(biom)) {
  install.packages('biom')
  library(biom)
}
if (!require(DT)) {
  install.packages('DT')
  library(DT)
}
if (!require(RColorBrewer)) {
  install.packages('RColorBrewer')
  library(RColorBrewer)
}
if (!require(gplots)) {
  install.packages('gplots')
  library(gplots)
}
if (!require(DESeq2)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("DESeq2")
  library(DESeq2)
}
if (!require(ade4)) {
  install.packages('ade4')
  library(ade4)
}
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sidebar <- dashboardSidebar(
  sidebarMenu(
    menuItem("Home", tabName = "Home", icon = icon("home")),
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
    menuItemOutput("dymMenu")
  )
)

body <- dashboardBody(
  tabItems(
    tabItem(tabName = "Home",
            h2("Bienvenue !")
    ),
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            fluidRow(
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              column(width=3,valueBoxOutput("valueErrorPercent",width=NULL)),
              column(width=3,infoBoxOutput("InfoErrorCounts",width=NULL)),
              column(width=3,infoBoxOutput("InfoErrorTaxo",width=NULL))
            ),
            br(),
             fluidRow(
                box(title="Select your file format",width = 3,status = "success", solidHeader = TRUE,collapsible = FALSE,
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                  selectInput("FileFormat","",c("Counts table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
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                ),
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                conditionalPanel(condition="input.FileFormat=='fileCounts'",
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                  box(title="Load the counts table",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
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                    fileInput('fileCounts', h6(strong('Select your file')),width="100%")
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                  ),
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                  box(title="Load the taxonomy file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
                      fluidRow(
                        column(width=6,radioButtons("TypeTaxo",h6(strong("Format:")),c("Table"="Table","RDP"="RDP"))),
                        column(width=6,
                             conditionalPanel(condition="input.TypeTaxo=='RDP'",numericInput("RDP_th",h6(strong("Threshold:")),0.5,step=0.01,min=0.01,max=1))
                        )
                      ),
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                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
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                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
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                                 box(title="Load the BIOM file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
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                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
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             ),
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              column(12,uiOutput("TabBoxData"))

              
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  #### Statistical analysis

    tabItem(tabName = "RunDiff",
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            fluidRow(
              column(width=3,infoBoxOutput("RowTarget",width=NULL)),
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
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              column(width=3,infoBoxOutput("InfoDESeq",width=NULL)),
              column(width=3,conditionalPanel(condition="input.RunDESeq>=1",infoBoxOutput("InfoContrast",width=NULL)))
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            ),            
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            fluidRow(
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              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
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                    column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
                    column(width=6,uiOutput("SelectTaxo"))
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                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
                    column(width=6,uiOutput("SelectInteraction2")),
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                    column(width=6,uiOutput("RunButton"))
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                  )
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                ),
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
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              ),
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              column(width=7,
                box(title="Options",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
                  fluidRow(
                    column(width=3,
                      radioButtons("TransType",h6(strong("Type of transformation")),choices = c("VST"="VST","rlog"="rlog"))
                    ), 
                    column(width=3,
                      radioButtons("IndFiltering",h6(strong("Independent filtering")),choices = c("True"=TRUE,"False"=FALSE))
                    ),
                    column(width=3,
                      radioButtons("AdjMeth",h6(strong("p-value adjustement")),choices = c("BH"="BH","BY"="BY"))
                    ),
                    column(width=3,
                      textInput("AlphaVal",h6(strong("Level of significance")),value=0.05)
                    )
                  ),
                  fluidRow(
                    column(width=3,
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                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
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                           conditionalPanel(condition="input.CooksCutOff=='val'",textInput("CutOffVal",h6("Cut-off:"),value=0))
                    ),
                    
                    column(width=3,
                      radioButtons("locfunc",h6(strong("Local function")),choices = c("Median"="median","Shorth"="shorth"))
                    ),  
                    column(width=3,
                      radioButtons("fitType",h6(strong("Relationship")),choices = c("Parametric"="parametric","Local"="local"))
                    ),
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                    column(width=3,
                      conditionalPanel(condition="input.FileFormat=='fileCounts' && input.TypeTaxo=='RDP'",
                        sliderInput("ThreshProba",h6(strong("Probability threshold (rdp annotation)")),min=0.01, max=1,value=0.5,step = 0.01)
                      )
                    ),
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                    column(width=3,uiOutput("RefSelect"))
                  )
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                ),
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                fluidRow(
                column(width=8,
                       uiOutput("contrastBox"),
                       uiOutput("contrastBoxAdvanced")
                       ),
                column(width=4,
                       uiOutput("contrastDefined")
                )  
                ) 
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              )
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            )
            
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    ),
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    tabItem(tabName = "DiagPlotTab",
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            fluidRow(
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              column(width=9,
                box(title = "Plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
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                  plotOutput("PlotDiag")
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                ),
                conditionalPanel(condition="input.DiagPlot=='Sfactors'",
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    dataTableOutput("SizeFactTable")
                  )
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                ),
                  
                conditionalPanel(condition="input.DiagPlot=='pcaPlot'",
                                 box(title = "Eigen values",  width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                                    plotOutput("PlotEigen")
                                 )
                ),
                conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
                                 box(title = "Eigen values",  width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                                     plotOutput("PlotpcoaEigen")
                                 )
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                )
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              ),
              column(width=3,
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                box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                    selectInput("DiagPlot",h6(strong("Select the plot")),c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
                                                                           "Maj. taxonomy"="MajTax", "Density"="densityPlot","Size factors"="Sfactors", 
                                                                           "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot",
                                                                           "SERE" = "SERE")),
                    conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
                                     h5(strong("Select the modalities")),
                                     uiOutput("ModMat"),
                                     selectInput("DistPCOA","Distance",c("euclidean", "canberra", "bray", "kulczynski", "jaccard", 
                                                              "gower", "altGower", "morisita", "horn","mountford","raup","binomial",
                                                              "chao","cao","mahalanobis"),selected="jaccard")
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                                     )
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#                 conditionalPanel(condition="input.RadioPlotBi=='Nuage'",selectInput("ColorBiplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%")),
#                 sliderInput("TransAlphaBi", "Transparence",min=1, max=100, value=50, step=1),
#                 conditionalPanel(condition="input.RadioPlotBi!='Nuage'", radioButtons("SensGraphBi","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
#                 conditionalPanel(condition="input.RadioPlotBi=='box'", checkboxInput("CheckAddPointsBoxBi","Ajouter les données",value=FALSE)) 
               ),
                box(
                  title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    conditionalPanel(condition="input.DiagPlot=='Sfactors'",
                                     h6(strong("Layout")),
                                     numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
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                    ),
                  conditionalPanel(condition="input.DiagPlot=='clustPlot'",
                                   h6(strong("Layout")),
                                   selectInput("typeHculst", h6("Type"),c("Horizontal"="hori","Fan"="fan")),
                                   checkboxInput("colorHC","Add color",value=TRUE)
                  ),
                  conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",  selectInput("labelPCOA","Label type",c("Group", "Sample"),selected="Group"),
                                   #checkboxInput("colorgroup","Same color for the group",value=FALSE),
                                   sliderInput("cexcircle", "Circle size",min=0,max=2,value = 0.9,step =0.1),
                                   sliderInput("cexpoint", "Point size",min=0,max=3,value = 1,step =0.1),
                                   sliderInput("cexstar", "Star height",min=0,max=1,value = 0.95,step =0.1)
                                   
                  ),
                  sliderInput("cexLabelDiag", "Label size",min=0,max=5,value = 1,step =0.1)
#                   sliderInput("heightDiag", "height",min=100,max=1500,value = 500,step =10),
#                   sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
                 
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              ),
              box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                  selectInput("Exp_format",h5(strong("Export format")),c("png"="png","pdf"="pdf","eps"="eps","svg"="svg"), multiple = FALSE),
                  fluidRow(
                  column(width=6,numericInput("heightDiagExport", "Height (in px)",min=100,max=NA,value = 500,step =1)),
                  column(width=6,numericInput("widthDiagExport", "Width (in px)",min=100,max=NA,value = 500,step =1))
                  ),
                  downloadButton("exportdiag", "Export")
                  
#                   downloadButton("exportPDFdiag", "Download pdf"),
#                   downloadButton("exportPNGdiag", "Download png"),
#                   downloadButton("exportEPSdiag", "Download eps"),
#                   downloadButton("exportSVGdiag", "Download svg"),
                  
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              )
            )
        )
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    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
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              column(width=9,uiOutput("TabBoxDataDiff")),
              column(width=3,
                     box(title = "Select your contrast",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                         selectInput("ContrastList_table",h6(strong("Contrast list")),"", multiple = FALSE),
                         htmlOutput("ContrastOverviewTable")
                      )
            )
            )
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    ),
  
  #### Data Viz
  
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  tabItem(tabName = "BarplotVisu",
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          fluidRow(
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            column(width=9,showOutput("PlotVisu")),

            column(width=3,
              box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                uiOutput("VarIntVisuBP"),
                uiOutput("TaxoToPlotBP"),
                radioButtons(inputId = "CountsOrProp",label = "Value: ",choices = c("Proportions" = "prop", "Counts" = "counts"),selected = "prop"),
                radioButtons(inputId = "SensPlotVisuBP",label = "Type: ",choices = c("Vertical" = "multiBarChart", "Horizontal" = "multiBarHorizontalChart"),selected = "multiBarChart")
              ),
              box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                sliderInput("heightVisu", h6(strong("Height")),min=100,max=2000,value = 800),
                sliderInput("widthVisu", h6(strong("Width")),min=100,max=1200,value = 1000)
              )
            )
          )
  ),
  

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tabItem(tabName = "HeatmapVisu",
        fluidRow(
          column(width=9,
                 #d3heatmapOutput(outputId ='d3heatmap', width = "1000p", height = "800px")
                 
                 plotOutput("heatmap")
                 
          ),
          column(width=3,
                 box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                     selectInput(inputId = "HeatMapType",label = h6(strong("Data")),choices = c("Counts" = "Counts", "Log2FC" = "Log2FC"),selected = "Counts"),
                     selectInput("ContrastList_table_FC",h6(strong("Contrast list")),"", multiple = TRUE),
                     uiOutput("VarIntVisuHM"),
                     uiOutput("TaxoToPlotHM"),
                     radioButtons(inputId = "SensPlotVisuHM",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical"),
                     selectInput(inputId = "scaleHeatmap",label = h6(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none"),
                     downloadButton("exportPDFVisu", "Download pdf")
                 ),
                 box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                     selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
                     sliderInput("heightHeat", h6(strong("Height")),min=100,max=2000,value = 800),
                     sliderInput("widthHeat", h6(strong("Width")),min=100,max=2000,value = 800),
                     sliderInput("LabelSizeHeatmap", h6(strong("Label size")),min=0.1,max=2,value = 0.7,step = 0.1),
                     sliderInput("LabelOrientHeatmap", h6(strong("Label orientation")),min=0,max=90,value = 0,step = 5),
                     sliderInput("LabelColOffsetHeatmap", h6(strong("Label column offset")),min=0,max=4,value = 0,step = 0.5),
                     sliderInput("LabelRowOffsetHeatmap", h6(strong("Label row offset")),min=0,max=4,value = 0,step = 0.5),
                     sliderInput("rightMargin", h6(strong("Right margin")),min=0,max=20,value = 6,step = 1),
                     sliderInput("lowerMargin", h6(strong("Lower margin")),min=0,max=20,value = 6,step = 1)
                     
                 )
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        )
        
),
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  tabItem(tabName = "BoxplotVisu",
          fluidRow(
            column(width=9,plotOutput("Boxplot"),                uiOutput("BoxCountsMerge_pierre")),
            
            #                    downloadButton("exportPDFVisu", "Download pdf"),
            #                    downloadButton("exportPNGVisu", "Download png")
            #)      
            
            column(width=3,
                   box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                       uiOutput("VarIntVisuBoxP"),
                       uiOutput("TaxoToPlotBoxP"),
                       selectInput("typeDataBox","Type of data",c("Log2"="Log2","Relative"="Relative")),
                       radioButtons(inputId = "SensPlotVisuBoxP",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical")
                   ),
                   box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                       #selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
                       sliderInput("heightBoxP", h6(strong("Height")),min=100,max=2000,value = 800),
                        checkboxInput("CheckAddPointsBox","Add points",value=TRUE)
                   
                   )
            )
          )
          
  ),

  tabItem(tabName = "DiversityVisu",
          fluidRow(
            column(width=9,plotOutput("DiversityPlot")
#                    conditionalPanel(condition="input.AddBoxplotDiv==TRUE",
#                                     plotOutput("DiversityBoxPlot")
#                    )
                   ),
            
            
            column(width=3,
                   box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                       uiOutput("VarIntVisuDiv"),
                       selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma'),selected  = c('Alpha','Beta','Gamma'),multiple=TRUE),
                       radioButtons(inputId = "SensPlotVisuGlobal",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical"),
                       checkboxInput("AddBoxplotDiv","AddBoxplot",value=FALSE),
                       conditionalPanel(condition="input.AddBoxplotDiv==TRUE",
                                        uiOutput("SelectVarBoxDiv")
                       )
                       #                      uiOutput("DiversityGroupBy")
                   ),
                   box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                       #selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
                       sliderInput("sizePointGlobal", h6(strong("Points size")),min=0.5,max=10,value =3,step=0.5),
                       checkboxInput("SplitVisuGlobal","Split diversity",value=FALSE)
                       
                   )
            )
          )
          
  ),

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  tabItem(tabName = "RarefactionVisu",
          fluidRow(
            column(width=9,
                   plotOutput("RarefactionPlot",
                              dblclick = "RarefactionPlot_dblclick",
                              brush = brushOpts(
                                id = "RarefactionPlot_brush",
                                resetOnNew = TRUE
                              )
                   ))
            
            
#             column(width=3,
#                    box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
# #                        uiOutput("VarIntVisuDiv"),
# #                        selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma'),selected  = c('Alpha','Beta','Gamma'),multiple=TRUE),
# #                        radioButtons(inputId = "SensPlotVisuGlobal",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical")
# #                        
# #                        #                      uiOutput("DiversityGroupBy")
#                    ),
#                    box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# #                        #selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
# #                        sliderInput("sizePointGlobal", h6(strong("Points size")),min=0.5,max=5,value = 1.5,step=0.5),
# #                        checkboxInput("SplitVisuGlobal","Split diversity",value=FALSE)
# #                        
#                    )
#             )
          )
          
  ),

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  #### Krona plot
  tabItem(tabName = "Krona",
          fluidRow(
            column(width=3,p("Krona plot"))      
          )  
  )       
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#              column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
#             ),
#             fluidRow(
# 
#               column(9,
#                      box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
#                       dataTableOutput("DataBrutes")
#                      )
#               ),
#               column(width=3,
#                      box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          h5(strong('Votre fichier contient t-il ...')),
#                          radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
#                          radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
#                      ),
#                      
#                      box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#               column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
#             ),
#             fluidRow(
# 
#               column(9,
#                      box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
#                       dataTableOutput("DataBrutes")
#                      )
#               ),
#               column(width=3,
#                      box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          h5(strong('Votre fichier contient t-il ...')),
#                          radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
#                          radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
#                      ),
#                      
#                      box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                      box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#               column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
#               column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
#             ),
#             fluidRow(
# 
#               column(9,
#                      box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
#                       dataTableOutput("DataBrutes")
#                      )
#               ),
#               column(width=3,
#                      box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          h5(strong('Votre fichier contient t-il ...')),
#                          radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
#                          radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
#                      ),
#                      
#                      box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          uiOutput("SelectDataVar"),
#                          actionButton("RefreshData",icon=icon("refresh"),strong("Actualiser"))
#                      ),
#                      
#                      box(title = "Transformer des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          uiOutput("SelectVarQuanti"),
#                          actionButton("GoQuali",icon=icon("arrow-circle-right"),strong("Transformer")),
#                          uiOutput("QuantiToQuali"))  
#               )
#             )
#             
#     ),
#     tabItem(tabName = "AnaStat",
#             
#           p("De nombreuses analyses statistiques peuvent être réalisées à partir de vos données. Decouvrez l'information
#             contenue dans vos données (analyse unvariée) et étudier les relations entre vos différentes variables.")
#     ),
#     
#     tabItem(tabName = "DescGene",
#             fluidRow(
#               
#               column(width=9,
#                      tabBox(side = "left",id = 'tabs', width=NULL, status = "primary",
#                                  tabPanel("Variables quantitatives",value=1,
#                                           h4(strong("Statistiques descriptives (variables quantitatives)")),
#                                           dataTableOutput("TableQuanti")
#                                         
#                                  ),
#                                  tabPanel("Variables qualitatives",value=2,
#                                           h4(strong("Statistiques descriptives (variables qualitatives)")),
#                                           dataTableOutput("TableQuali")
#                                  ),
#                                  tabPanel("Table des corrélations",value=3,
#                                           h4(strong("Table des corrélations")),
#                                           dataTableOutput("CorTable")
#                                  )
# 
#                                  
#                      ),
#                      
#                      conditionalPanel(condition="input.TestCor==true",
#                                       box(title="Résultat du test",width = NULL, status = "success", solidHeader = TRUE,collapsible = TRUE,
#                                                dataTableOutput("CorTableTest")
#                                                
#                                                
#                                       ))
#               ),
#               column(width=3,
#                      box(title = "Choix de l'analyse", width = NULL, status = "primary", solidHeader = TRUE,
#                          conditionalPanel(condition = "input.tabs==1",
#                                           selectInput("IndicQuanti",p(strong("Choisissez les indicateurs"),h6(em("Sélection multiple avec CTRL"))),
#                                                       c("Nb valeurs"=1,
#                                                         "Nb manquants"=2,
#                                                         "Somme"=3,
#                                                         "Min"=4,
#                                                         "1er Quartile"=5,
#                                                         "Mediane"=6,
#                                                         'Moyenne'=7,
#                                                         "3eme Quartile"=8,
#                                                         "Max"=9,
#                                                         "Variance"=10,
#                                                         "Ecart-type"=11,
#                                                         "Coeff Variation"=12),
#                                                       selected=c(1,2,3,4,5,6,7,10),multiple=TRUE,size=2,selectize=FALSE),
#                                           actionButton("RefreshStat",icon=icon("refresh"),strong("Refresh"))
#                          ),
#                          conditionalPanel(condition = "input.tabs==2",
#                                           selectInput("IndicQuali",p(strong("Choisissez les indicateurs"),h6(em("Sélection multiple avec CTRL"))),
#                                                       c("Effectifs"=1,
#                                                         "%"=2,
#                                                         "% cumulés"=3),
#                                                       selected=c(1,2,3),multiple=TRUE,size=2,selectize=FALSE),
#                                           actionButton("RefreshStatQuali",icon=icon("refresh"),strong("Refresh"))
#                          ),
#                          
#                          conditionalPanel(condition = "input.tabs==3",
#                                           radioButtons("CorelMeth","Choix de la corrélation",
#                                                        choices=c("Pearson"="pearson","Spearman"="spearman","Kendall"="kendall")),
#                                           checkboxInput("TestCor","Test de corrélation",value=FALSE)
#                          )
#                      ),
#                      box(title = "Aide", width = NULL, status = "warning", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE
#                      )
#               )
#             )
#     ),
#     
#     tabItem(tabName = "AnalUni",
#             fluidRow(
#               column(width = 9,
#               box(
#                 title = "Représentation",status = "success", solidHeader = TRUE,collapsible = TRUE,width=NULL,
#                 plotOutput("plotuni"),
#                 p(Align='right',
#                   downloadButton("exportPDFuni", "Download pdf"),
#                   downloadButton("exportPNGuni", "Download png")
#                 )
#               ),
#               conditionalPanel(condition="input.TestMoyCible==true", infoBoxOutput("ResTTestBox",width=6))    
#             ),
#             column(width = 3,
#                        box(
#                          title = "Choix de l'analyse", width = NULL, status = "primary", solidHeader = TRUE,
#                          
#                          uiOutput("SelectUniVar"),
#                          uiOutput("RadioUniPlot"),
#                          checkboxInput("TestMoyCible","T-test",value=FALSE),
#                          conditionalPanel(condition="input.TestMoyCible==true", 
#                                           textInput("ValCibleTtest", label ="Valeur cible", value = 0,width="50%"),
#                                           textInput("alphaTtest", label ="Seuil (en %)", value = 5,width="50%"),
#                                           actionButton("ExecuteTtestCible",icon=icon("sign-in"),strong("Exécuter"))
#                          )
#                        ),
#                        box(
#                          title = "Options du graphique",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                          
#                          conditionalPanel(condition="input.RadioPlotUni=='BarPlot'",sliderInput("widthBarPlot", "Taille des barres",min=1, max=100, value=50, step=1)),
#                          conditionalPanel(condition="input.RadioPlotUni=='Pie'", sliderInput("PieWidth", "Largeur", min=1, max=100, value=100, step=1)),
#                          conditionalPanel(condition="input.RadioPlotUni!='Pie'", sliderInput("SizeQQplot", "Taille",min=1, max=10, value=2, step=0.5)),
#                          
#                          selectInput("ColorUniplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%"),
#                          sliderInput("TransAlphaUni", "Transparence",min=1, max=100, value=50, step=1),
#                          conditionalPanel(condition="input.RadioPlotUni=='hist'",sliderInput("binwidth", "Taille de la fenètre glissante",min=1, max=100, value=1, step=1)),
#                          conditionalPanel(condition="input.RadioPlotUni=='hist'", radioButtons("HistDens","Ordonnées",choices=c("Comptages"="counts","Fréquences"="freq"))),
#                          conditionalPanel(condition="input.RadioPlotUni=='hist'", checkboxInput("CheckDens","Ajouter la densité",value=FALSE)),
#                          conditionalPanel(condition="input.RadioPlotUni!='qqplot'", radioButtons("SensGraph","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
#                          conditionalPanel(condition="input.RadioPlotUni=='box'", checkboxInput("CheckAddPointsBox","Ajouter les données",value=FALSE)),
#                          conditionalPanel(condition="input.RadioPlotUni=='BarPlot'",checkboxInput("BarCircular","Représentation circulaire",FALSE))
#                          
#                        )
#               )
#             )
#             
#             
#             
#             ),
#     
#     tabItem(tabName = "AnalBi",
#     
#             fluidRow(
#               column(width=9, 
#                      box(
#                        title = "Représentation",  width = NULL, status = "success", solidHeader = TRUE,collapsible = TRUE,
#                        
#                      plotOutput("biplot",
#                                 dblclick = dblclickOpts(
#                                   id = "biplot_dblclick"
#                                 ),
#                                 hover = hoverOpts(
#                                   id = "biplot_hover"
#                                 ),
#                                 brush = brushOpts(
#                                   id = "biplot_brush",
#                                   resetOnNew = TRUE
#                                 )    
#                      ),
#                      p(Align='right',
#                      downloadButton("exportPDFbi", "Download pdf"),
#                      downloadButton("exportPNGbi", "Download png")
#                      )
#                      ),
#                      conditionalPanel(condition="input.TestMoy==true", infoBoxOutput("ResTTest2sampBox",width=6)), 
#                      conditionalPanel(condition="input.RadioPlotBi=='Nuage'",infoBoxOutput("biplot_info",width=6))
#               ),
#               column(width=3,
#                      box(
#                      title = "Choix de l'analyse",  width = NULL, status = "primary", solidHeader = TRUE,
#                        
#                      uiOutput("SelectDataVarBi1"),
#                      uiOutput("SelectDataVarBi2"),
#                      uiOutput("RadioBiPlot"),
#                      uiOutput("CheckTestBi"),
#                      conditionalPanel(condition="input.TestBi!=''",textInput("alphaTtestMoy", label ="Seuil (en %)", value = 5,width="50%")),
#                      conditionalPanel(condition="input.RadioPlotBi=='Nuage'", h5(strong("Modèle linéaire")),checkboxInput("CheckLM", "Droite de régression",value = FALSE))
#                      
#                      ),
#                      box(
#                        title = "Options du graphique",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#                        
#                        sliderInput("SizePoint", "Taille",min=1, max=10, value=2, step=0.5),
#                        conditionalPanel(condition="input.RadioPlotBi=='hist'",sliderInput("binwidthBi", "Taille de la fenètre glissante",min=1, max=100, value=1, step=1)),
#                        conditionalPanel(condition="input.RadioPlotBi=='Nuage'",selectInput("ColorBiplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%")),
#                        sliderInput("TransAlphaBi", "Transparence",min=1, max=100, value=50, step=1),
#                        conditionalPanel(condition="input.RadioPlotBi!='Nuage'", radioButtons("SensGraphBi","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
#                        conditionalPanel(condition="input.RadioPlotBi=='box'", checkboxInput("CheckAddPointsBoxBi","Ajouter les données",value=FALSE))
#                        
#                      )
#                    
#               )
#               
#               
#               
#             )
             )
     
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  )
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# Put them together into a dashboardPage
dashboardPage(skin="blue",
  dashboardHeader(title = "Meta16S"),
  sidebar,
  body
)