ui.R 25.7 KB
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library(shinydashboard)
library(DT)
library(biom)

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$style(type='text/css', ".well { max-width: 20em; }"),
            # Tags:
            tags$head(
              tags$style(type="text/css", "select[multiple] { width: 100%; height:10em}"),
              tags$style(type="text/css", "select { width: 100%}"),
              tags$style(type="text/css", "input { width: 19em; max-width:100%}")
            ),
            fluidRow(
              column(12,
                  h3(strong("Instructions")),
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                  p("Décrire le format des différents fichiers"),
                  p("Décrire le format des différents fichiers"),
                  p("Décrire le format des différents fichiers"),
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                  p("Décrire le format des différents fichiers")
              ),
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              br(),
              
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              column(3,
                box(title="Select your file format",width = NULL, 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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                #uiOutput("LoadButton")
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              ),
              column(9,
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
                  box(title="Load the counts table",width = 4, 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 = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
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                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
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                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
                                 box(title="Load the BIOM file",width = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
                
              ),
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              column(12,uiOutput("TabBoxData"))

              
          )
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    ),
    
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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("InfoContrast",width=NULL)),
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL))
            ),
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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")),
                    column(width=6,actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right")))
                  )
                )
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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,
                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='NULL',"No cut-off"=Inf,"Value"="val")),
                           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"))
                    ),
                    column(width=3,uiOutput("RefSelect"))
                  )
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                ),
                uiOutput("BoxTarget")
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              )
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            ),
            
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            fluidRow(
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              column(width=12,
                box(title="Contrasts",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
                    column(width=3,uiOutput("contrastMat")),
                    column(width=3,
                      textInput("ContrastName","Contrast name","Name..."),
                      actionButton("AddContrast","Add contrast",icon = icon("plus"))
                    ),
                    column(width=3,
                      selectInput("ContrastList","Contrasts","",multiple=TRUE,size=2,selectize=FALSE),
                      actionButton("RemoveContrast","Remove",icon = icon("remove"))
                    ),
                    column(width=3,
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                      h5(strong("Selected contrast:")),
                      htmlOutput("ContrastOverview")
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                    ) 
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                )
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              )  
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            )
            
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    ),
    tabItem(tabName = "DiagPlot",
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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,
                  plotOutput("PlotDiag"),  
                  p(Align='right',
                    downloadButton("exportPDFdiag", "Download pdf"),
                    downloadButton("exportPNGdiag", "Download png")
                  )
                ),
                
                br(),
                conditionalPanel(condition="input.DiagPlot=='Sfactors'",
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    dataTableOutput("SizeFactTable")
                  )
                )
              ),
              column(width=3,
                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")),
                    conditionalPanel(condition="input.DiagPlot!='pcaPlot' && input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntBarPlot"))
                    
#                 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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    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
              column(width=3,p("Table of differential abundance"))         
            )  
    ),
  
  #### Data Viz
  
  tabItem(tabName = "Visu",
          fluidRow(
            column(width=3,p("Visualisation"))    
          )  
  ),
  
  
  #### 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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# Put them together into a dashboardPage
dashboardPage(skin="blue",
  dashboardHeader(title = "Meta16S"),
  sidebar,
  body
)