inst/shiny/ui.R

In CrossICC: An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

options(spinner.type=4)

#required packages
suppressMessages(library(shiny))
suppressMessages(library(shinydashboard))
suppressMessages(library(shinyWidgets))
suppressMessages(library(shinycssloaders))
suppressMessages(library(DT))


#sider bar----

sidebar <- dashboardSidebar(width = 300,
                            sidebarMenu(id="sidername",selected='home',
                                        menuItem("Home", tabName = "home", icon = icon("home")),
                                        menuItem("CrossICC result viewer", icon = icon("eye"),tabName = "CrossICC"),
                                        menuItem("Allocate New Sample", icon = icon("location-arrow"),tabName = "predict" ),
                                        menuItem('Correlation analysis', tabName = 'correlation',icon = icon("th",lib = "glyphicon")),
                                        menuItem('ssGSEA analysis', tabName = 'ssgsea',icon = icon("bar-chart")),
                                        menuItem('Survival analysis', tabName = 'Survival',icon = icon("line-chart"))
                            )
)


#bodyHome ----

bodyHome <- tabItem("home",
                    fluidRow(
                      box(
                        width = 12,
                        status = "success",
                        solidHeader = TRUE,
                        title = strong("Wellcome to the CrossICC reporter"),
                        includeMarkdown("dom/Readmeshiny.md")
                      )
                    ),

                    fluidRow(
                      box(
                        width = 4,
                        status = "info",
                        solidHeader = TRUE,
                        title =  strong("CrossICC result viewer"),
                        p("This module provide several plot functions to help inteprate CrossICC result."),
                        img(src = "images/home_crossICC.png", align = "center", width="100%")
                      ),
                      box(
                        width = 4,
                        status = "info",
                        solidHeader = TRUE,
                        title =  strong("New sample allocator"),
                        p("After obtain a cluster system based on trained data, it would be applicable if we are going to allocate new samples.
                          In this module, users are encoraged uploading expression data of testing samples to figure out which cluster they belong to."),
                        img(src = "images/workflow.png", align = "center", width="100%")
                      ),
                      box(
                        width = 4,
                        status = "info",
                        solidHeader = TRUE,
                        title =  strong("Cancer related analysis functions"),
                        includeMarkdown("dom/home_cancerR.md"),
                        img(src = "images/cancerRelated.png", align = "center", width="100%")
                      )
                    ),
                    fluidRow(
                      box(
                        width = 12,
                        status = "warning",
                        solidHeader = TRUE,
                        title =  strong("Citation"),
                        h4("If you use CrossICC, please cite this paper:"),
                        p("Preparing in process")
                      )
                    ))

#bodyCrossICC ----

bodyCrossICC <- tabItem("CrossICC",
                        h2("Visualize CrossICC object"),
                        fluidRow(
                          #setting panel
                          box(
                            title = div(shiny::icon("gear"), "Data upload & Configuration", inline =TRUE),
                            width = 3,
                            tabBox (
                              height = "100%", width = "100%",
                              id = "crossICCsettingPanel",
                              title = "",
                              side = "left",
                              selected = "crs01",
                              tabPanel(
                                title = div(icon("book"), "Upload"),
                                value = "crs01",
                                  radioButtons(
                                    "dataset",
                                    strong("Loading CrossICC output"),
                                    inline = TRUE,
                                    c(Default = "default", Upload = "upload"),
                                    selected = 'default'
                                  ),
                                  conditionalPanel(
                                    condition = "input.dataset == 'upload'",
                                    fileInput(
                                      'file1','CrossICC output data in RDS format',accept = c('application/rds', '.rds')
                                    )
                                  ),
                                  actionBttn("submit", div(
                                    "Click ME to visualize result ",
                                    icon("hand-right", lib = "glyphicon")
                                  )),

                                  div(align = 'center',h4("Your running parameters "), tableOutput("outputArguments"))
                                  ),
                              tabPanel(
                                title = div(icon("book"), "Setting"),
                                value = "crs02",
                                fluidRow(
                                  switchInput(
                                    inputId = "clusterRow",
                                    label = "Cluster by Rows",
                                    value = FALSE
                                  ),
                                  switchInput(
                                    inputId = "showRowNames",
                                    label = "show row names",
                                    value = FALSE
                                  )
                                ),
                                sliderInput("cross_size", "Zoom in/out graph:",min = 500, max = 1000, value = 800)
                              )
                            )
                          ),
                          box(
                            width = 9,
                            title = "Visualization",
                            tabBox (
                              height = "100%", width = "100%",
                              id = "crossICCresultPanel",
                              side = "left",
                              selected = "cr06",
                              tabPanel(
                                title = div(icon("book"), "Summary"),
                                value = "cr01",
                                dataTableOutput("OutputResultSignature"),
                                box(
                                  width = NULL,  status = "success",
                                  h4("Download Clustering result"),
                                  downloadButton("OutputClusterResult"),
                                  h4("Gene signature for each cluster"),
                                  downloadButton("geneSignature", label = "Download Matrix")
                                  )

                              ),
                              tabPanel(
                                title = div(icon("th", lib = "glyphicon"), "Super Clustering"),
                                value = "cr02",

                                withSpinner(plotOutput("superclusterPlot", height = "100%"), color = "black"),
                                box(
                                  width = NULL,  status = "success",
                                  radioButtons("DownloadSuperclusterPlotCheck","Choose file type to download:",
                                    c("png", "pdf", "tiff"),inline = TRUE
                                  ),
                                  downloadButton('DownloadSuperclusterPlot', 'Download')
                                )
                              ),
                              tabPanel(
                                title = div(icon("signal", lib = "glyphicon"), "Silhouette Result"),
                                value = "cr03",

                                withSpinner(plotOutput("Silhouette",height = "100%"), color = "black")
                                ,
                                box(
                                  width = NULL,  status = "success",
                                  radioButtons("DownloadSilhouetteCheck","Choose file type to download:",
                                                     c("png", "pdf", "tiff"),inline = TRUE
                                  ),
                                  downloadButton('DownloadSilhouette', 'Download Plot')
                                  )

                              ),
                              tabPanel(
                                title = div(icon("book"), "Expression heatmap by signagure"),
                                value = "cr04",


                                uiOutput("expressionHeatmapSelectPlatform"),
                                withSpinner(plotOutput("clusterexpress",height = "100%"), color = "black"),
                                box(
                                  width = NULL,  status = "success",
                                  radioButtons("DownloadClusterexpressPlotCheck","Choose file type to download:",
                                                     c("png", "pdf", "tiff"),inline = TRUE
                                  ),
                                  downloadButton('DownloadClusterexpressPlot', 'Download Plot'),
                                  downloadButton('DownloadClusterExpressMatrix', 'Download Matrix')
                                )
                              ),
                              tabPanel(
                                title = div(icon("book"), "Iteration Record"),
                                value = "cr05",
                                plotOutput("IterationPlot", height = "100%"),
                                box(
                                  width = NULL,  status = "success",
                                  radioButtons("DownloadIterationPlotCheck","Choose file type to download:",
                                                     c("png", "pdf", "tiff"),inline = TRUE
                                  )
                                # to be added
                                )
                              ),
                              tabPanel(
                                title = div(icon("book"), "Readme"),
                                value = "cr06",
                                includeMarkdown("dom/CrossICCObject.Rmd")
                              )
                            )
                          )
                        ))

#bodyPredict----

bodyPredict <- tabItem(
  "predict",
  h2("Allocate new samples with their expression value"),
  fluidRow(
    #setting panel
    box(
      title = "Input your data set for prediction",
      background = "black",
      width = 3,
      radioButtons(
        "dataset2",
        strong("Data to predict"),
        inline = TRUE,
        c(Default = "default", Upload = "upload"),
        selected = 'default'
      ),
      conditionalPanel(
        condition = "input.dataset2 == 'upload'",
        fileInput(
          'file2',
          'Input dataset in matrix file',
          accept = c('text/txt', '.rds')
        )
      ),
      actionBttn("submit2", "Submit")
    ),
    tabBox (
      id = "PredictResultPanel",
      title = h3("Analysis"),
      width =9,
      side = "right",
      selected = "pre02",
      tabPanel(
        title = div(icon("book"), "PredictResult"),
        value = "pre01",

        downloadLink('DownloadPredictHeatmap', 'Download PDF'),
        withSpinner(plotOutput("predictHeatmap", height = "800px"), color = "black")

      ),
      tabPanel(
        title = div(icon("book"), "Readme"),
        value = "pre02",
        includeMarkdown("dom/predict.Rmd")
      )
    )
  )

)

# bodyCorrelation----

bodyCorrelation <- tabItem(
  "correlation",
  h2("Correlation analysis of the two cluster system"),
  fluidRow(
    valueBoxOutput("getRAbox", width = 4),
    valueBoxOutput("getARIbox", width = 4),
    valueBoxOutput("getJaccarddox", width = 4)

  ),

  fluidRow(
    box( width = 3,
         title = "Analysis",
          tabBox (
            height = "100%", width = "100%",
            selected = "caInput01",
            side = "left",
            tabPanel(
              title = div(icon("table"), "Data Input"),
              value = "caInput01",
              radioGroupButtons(
                "data3",
                label = strong("clinical Dataset"),
                choices = c(Default = "Default", Upload = "Upload"),
                selected = 'Default',
                status = "primary"
              ),
              conditionalPanel(
                condition = "input.data3 == 'Upload'",
                fileInput(
                  'file3',
                  'Input dataset in matrix file',
                  accept =
                    c('text/txt', '.csv')
                )
              ),
              uiOutput("VariableSelectionUI1"),
              uiOutput("VariableSelectionUI2"),
              actionBttn("submit3", "Submit", style = "unite")

            ),
            tabPanel(
              title = div(icon("cog"), "Setting"),
              value = "caInput01",
              selectInput("cor_theme", "Plot Theme:",
                          c("default","Tufte","Economist","Solarized","Stata","Excel 2003","Inverse Gray","Fivethirtyeight","Tableau","Stephen","Wall Street","GDocs","Calc","Pander","Highcharts"))
              ,
              sliderInput("corre_size", "Zoom in/out graph:",min = 500, max = 1000, value = 800)
              )
          )
    ),

    box( width =9,
         title = "Analysis",
         tabBox (
           height = "100%", width = "100%",
           id = "clinicalResultPanel",
           side = "left",
           selected = "ca04",
           tabPanel(
             title = div(icon("book"), "Data"),
             value = "ca01",
             h3("Input Data "),
             dataTableOutput("summaryCorrelationData")
           ),
           tabPanel(title = div(icon("book"), "Contingency Table "),
                    value ="ca02",
                    dataTableOutput("ContingencyTableRender")

           ),
           tabPanel(
             title = div(icon("book"), "Plot"),
             value = "ca03",
             withSpinner(plotOutput("getCorplotRender",height = "100%"), color = "black"),
             box(
               width = NULL,  status = "success",
               radioButtons("DownloadCorrelationPlotCheck","Choose file type to download:",
                            c("png", "pdf", "tiff"),inline = TRUE,selected = "pdf"
               ),
               downloadBttn('DownloadCorrelationPlot', 'Download')
               # to be added
             )
           ),
           tabPanel(
             title = div(icon("book"), "SankeyPlot"),
             value = "ca04",
             withSpinner(plotOutput("getSankyPlotRender",height = "100%"), color = "black"),
             box(
               width = NULL,  status = "success",
               radioButtons("DownloadsankeyPlotCheck","Choose file type to download:",
                            c("png", "pdf", "tiff"),inline = TRUE,selected = "pdf"
               ),
               downloadBttn('DownloadSankeyPlot', 'Download')
               # to be added
             )
           ),
           tabPanel(
             title = div(icon("book"), "Read Me"),
             value = "ca04",
             includeMarkdown("dom/correlation.Rmd")
             # ,includeHTML("dom/correlation.html")

           )
         )
    )

  )
)

# bodySsGSEA ----
bodySsGSEA <- tabItem("ssgsea",
                      h2("ssGSEA analysis"),
                      fluidRow(
                        #setting panel
                        box(
                          title = "Input dataset",
                          width = 3,
                          tabBox (id = "ssGseaSettingPanel",side = "left", selected = "ssgseaset01",
                                  height = "100%", width = "100%",
                            tabPanel(
                              title = div(icon("book"), "Loading"),
                              value = "ssgseaset01",
                              # ssgsea data
                              radioGroupButtons(
                                "ssGSEAdata",
                                label = strong("Expression Data"),
                                choices = c(Example = "Example", Upload = "Upload"),
                                selected = 'Example',
                                status = "primary"
                              ),
                              conditionalPanel(
                                condition = "input.ssGSEAdata == 'Upload'",
                                fileInput(
                                  'ssGSEAdatafile',
                                  'Input dataset in matrix file',
                                  accept =
                                    c('text/txt', '.csv')
                                )
                              ),
                              radioGroupButtons(
                                "ssGSEASet",
                                label = strong("GENE SET"),
                                choices = c(KEGG = "KEGG",Default= "Default",Upload = "Upload"),
                                selected = 'Default',
                                status = "primary"
                              ),
                              conditionalPanel(
                                condition = "input.ssGSEASet == 'Upload'",
                                fileInput(
                                  'ssGSEAgenesetfile',
                                  'Input Geneset file',
                                  accept =
                                    c('text/txt', '.csv')
                                )
                              )


                            ),
                            tabPanel(
                              title = div(icon("book"), "Setting"),
                              value = "ssgseaset02",
                              sliderInput("ssgsea_size", "Zoom in/out graph:",min = 500, max = 1000, value = 800)

                            )
                          )
                        ),
                        box(
                          title = "Analysis Result",
                          width =9,
                          tabBox (
                            height = "100%", width = "100%",
                            id = "ssGseaResultPanel", side = "left",selected = "ssgseaRes03",
                            tabPanel(
                              title = div(icon("book"), "Out Table"),
                              value = "ssgseaRes01",
                              dataTableOutput("ssGSEAmatrix")

                            ),
                            tabPanel(
                              title = div(icon("book"), "Plot"),
                              value = "ssgseaRes02"

                            ),
                            tabPanel(
                              title = div(icon("book"), "Read Me"),
                              value = "ssgseaRes03"
                               ,includeMarkdown("dom/ssGSEA.Rmd")
                            )
                          )
                        )
                      ))

# bodySurvival ----
bodySurival <- tabItem(
  "Survival",
  h2("Survival evaluation of the clustering system"),
  fluidRow(
    #setting panel
    box(
      title = "Input dataset",
      width = 3,
      tabBox (id = "SurvivalSettingPanel" , side = "left",selected = "survivalset01",
              height = "100%", width = "100%",
              tabPanel(
                title = div(icon("book"), "Loading"),
                value = "survivalset01",
                radioGroupButtons(
                  "data5",
                  label = strong("Survival Dataset"),
                  choices = c(Default = "Default", Upload = "Upload"),
                  selected = 'Default',
                  status = "primary"
                ),
                conditionalPanel(
                  condition = "input.data5 == 'Upload'",
                  fileInput(
                    'survivalFile',
                    'Input dataset in matrix file',
                    accept =
                      c('text/txt', '.csv')
                  )
                ),
                
                uiOutput("survivalFeatureSelect1"),
                uiOutput("survivalTimeSelect1"),
                uiOutput("survivalStatusSelect1"),
                actionBttn("submit5", "Submit", style = "unite")


              ),
              tabPanel(
                title = div(icon("book"), "Setting"),
                value = "survivalset02",

                sliderInput("survival_size", "Zoom in/out graph:",min = 500, max = 1000, value = 800)

              )
      )
    ),
    box(
      title = "Analysis Result",
      width =9,
      tabBox (id = "survivalResultPanel",   side = "left", selected = "survivalRes03",
              height = "100%", width = "100%",
              
              tabPanel(
                title = div(icon("book"), " Dataset"),
                value = "survivalRes01",
                dataTableOutput("survivalData")
                # , includeHTML("dom/survival.html")
              ),
    
              tabPanel(
                title = div(icon("book"), "Plot"),
                value = "survivalRes02",
                withSpinner(plotOutput("SurvivalPlotRender",height = "100%"), color = "black"),
                box(
                  width = NULL,  status = "success",
                  radioButtons("DownloadSurvivalPlotCheck","Choose file type to download:",
                               c("png", "pdf", "tiff"),inline = TRUE,selected = "pdf"
                  ),
                  downloadBttn('DowloadSurvival', 'Download')
                  # to be added
                )
      
              ),
              tabPanel(
                title = div(icon("book"), "Read Me"),
                value = "survivalRes03",
                includeMarkdown("dom/survival.Rmd")
                # , includeHTML("dom/survival.html")
              )
      )
    )
  )
)

#-----------






#Main function----
shinyUI(dashboardPage(skin = "black",


  dashboardHeader(title = "CrossICC: iterative consensus clustering of cross-platform data",
                  titleWidth = 600
                  ),
  sidebar,
  dashboardBody(
    tags$head(
      tags$style(HTML("
      .shiny-output-error-validation {
                      color: brown;
                      }
                      ")),
      tags$link(rel = "stylesheet", type = "text/css", href = "css/main.css")
    ),
    tabItems(
      bodyHome,
      bodyCrossICC,
      bodyPredict,
      bodyCorrelation,
      bodySsGSEA,
      bodySurival

    )
  )
))