inst/shinyApp/app/ui.R

In Selkie-13/Jarvis:

dashboardPage(
  dashboardHeader(
    title="J.A.R.V.I.S."
  ),
  dashboardSidebar(
    tags$head(tags$link(rel = "stylesheet", type = "text/css", href = "style.css")),
    shinyjs::useShinyjs(),
    sidebarMenu(id="tab",
      menuItem("Upload Data",tabName="upload",icon=icon("dashboard")),
      menuItem("Preprocessing",icon=icon("wrench"),tabName="preprocess_auto"),
      menuItem("Annotation",icon=icon("wrench"),tabName="annotation"),
      menuItem("Download Data",tabName="download",icon=icon("dashboard")),
      column(12,verbatimTextOutput('ex_out')),
      column(12,downloadButton("save","Save"))
    )
  ),
  dashboardBody(
    add_busy_spinner(spin = "fading-circle"),
    tabItems(
      tabItem(tabName="upload",
        box(width=12,
          column(4,fileInput("fcs","Upload FCS file(s)",multiple=TRUE, accept=c(".csv"))),
          column(2,tags$br(),actionButton("refresh_input","Refresh")),
          column(3,fileInput("jarvis_load","Upload .Jarvis file",multiple=FALSE,accept=c(".jarvis")))
        ),
        box(width=12,
          dataTableOutput("summaryTable")
        )
      ),
      tabItem(tabName="preprocess_auto",conditionalPanel(condition="output.files_validate",
        column(3,
          box(width = 12, title = "Compensation",collapsible=TRUE,
            column(8,fileInput("spill","Comp CSV",multiple=FALSE,accept=c(".csv"))),
            column(4,selectInput("comp_key","Keywords",choices="none",multiple=FALSE)),
            column(12,actionButton("compenser","Compenser"))
          ),
          box(width=12,title="Transformation",collapsible=TRUE,
            column(6,selectInput("trans_method","Methode",choices=c("arcsinh","logicle","none"),multiple=FALSE,selected="none")),
            column(6,numericInput("trans_arg", "Arguments",value=NULL,step=1)),
            column(12,selectInput("trans_marker","Markers",choices=NULL,multiple=TRUE)),
            column(12,actionButton("transformer","Transformer"))
          ),
          box(width=12,title="Concantenation",collapsible=TRUE,
            column(6,textInput("concat_params","Nom",value="Jarvis.Flag")),
            column(6,tags$br(),actionButton("concatener","Concatener"))
          )
        ),
        column(9,
          box(width=12, title="Cleanning",collapsible=TRUE,
            column(12,selectInput("clean_method","Methode",choices=c("none","flowAI","flowClean","flowCut"),multiple = FALSE, selected="none")),
            column(6,uiOutput("clean_stat")),
            column(6,uiOutput("clean_plot")),
            column(12,actionButton("nettoyer","Nettoyer"))
          ),
          box(width=12, title="Normalize",collapsible=TRUE,
            column(2,
              selectInput("norm_methode","Methode",choices=c("none","gaussNorm")),
              selectInput("norm_markers","Markers",choices=c(NULL),multiple=TRUE)
            ),
            column(10,plotOutput("norm_plot")),
            column(12,actionButton("normaliser","Normaliser"))
          )
        )
      )),
      tabItem(tabName="annotation")
    )
  )
)