R/app_ui.R

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

#' @import shiny
app_ui <- function(request) {
  tagList(
    # Leave this function for adding external resources
    golem_add_external_resources(),
    
    navbarPage(title = tags$b("mSigAct"), id = "panels",
      tabPanel(title = tags$b("Home"), 
               HomeUI()),
      tabPanel(title = tags$b("Generate spectrum", 
                              tags$br(), "catalogs from VCFs"),
               UploadVCFUI(), 
               value = "generateCatalogTab"),
      tabPanel(title = tags$b("Upload spectra for", tags$br(),
                              "signature attribution"), 
               UploadSpectraUI(), 
               value = "uploadSpectraTab"),
      tabPanel(title = tags$b("Guides", tags$br(), 
                              "(help)"), 
               TutorialUI(),
               value = "tutorialTab"),
      position = "fixed-top",
      windowTitle = "mSigAct: Mutational Signature Activity")
  )
}

#' @import shiny
TutorialUI <- function() {
  #general.guide.path <- system.file("tutorial/top.help.md", 
  #                                  package = "mSigAct.server")
  fluidPage(
    tabsetPanel(
      id = "helpPages", 
      tabPanel(title = tags$b("General guide"),
               includeMarkdown(path = "inst/guides/general.guide.md")),
      tabPanel(title = tags$b("Guide to generating catalogs"),
               includeMarkdown(
                 path = "inst/guides/Guide.to.generating.catalogs.md")),
      tabPanel(title = tags$b("Guide to signature attribution"),
               includeMarkdown(
                 path = "inst/guides/Guide.to.signature.attribution.md"))
    ) # tabsetPanel
  ) # fluidPage
}

#' @import shiny
AttributionResultsUI <- function() {
  fluidPage(
    br(),
    fluidRow(splitLayout(cellWidths = c("25%", "25%", "17.5%", "20%"),
                         actionButton(inputId = "analyzeMoreSample", 
                                      label = "Do another signature attribution",
                                      style = "color: #fff; background-color: #337ab7;
                             border-color: #2e6da4;"),
                         downloadButton(outputId = "downloadExposureTable", 
                                        label = "Download exposure counts"),
                         downloadButton(outputId = "downloadPdf",
                                        label = "Download PDF"),
                         downloadButton(outputId = "downloadMAPTable",
                                        label = "Download diagnostics"))),
    br(),
    DT::dataTableOutput(outputId = "exposureTable"),
    
  )
}

#' @import shiny
HomeUI <- function() {
  # List the first level UI elements here
  fluidPage(
    # Add a title on top the page
    titlePanel(title = p("mSigAct: Mutational Signature Activity",
                         style = "color: #337ab7"),
               windowTitle = paste0("mSigAct: Mutational Signature Activity")),


    # Add one line break
    # br(),

    # Add a short description of msigact
    h4("This web site has two main functions:"),

    h4(tags$ol(
      tags$li(actionLink(
        inputId = "linkToGenerateCatalogTab",
        label = "Generate mutational spectrum catalogs from VCFs* and plot them")),
      br(),
      tags$li(actionLink(
        inputId = "linkToUploadSpectraTab",
        label = paste0("Signature attribution: ", 
                       "Estimate which mutational signatures contributed to a ",
                       "mutational spectrum"))),
    )),
    
    h4(a(href = "https://tinyurl.com/rdzwnxd", "*VCFs", target = "_blank"),
       " are file that contain one mutation per line, and are created ",
      "by variant callers such as ",
      a(href = "https://github.com/Illumina/strelka", "Strelka", target = "_blank"), 
      " or ",
      a(href = "https://github.com/broadgsa/gatk", "Mutect", target = "_blank")),
    
    hr(),
    h4("mSigAct webserver can be freely accessed at ", 
       a(href = "https://msigact.ai",
         "https://msigact.ai", target = "_blank")),
    
    h4("To report issues, make suggestions, and request help, ",
       "post on ",
       a(href = "https://github.com/steverozen/mSigAct.server/issues",
         "GitHub", target = "_blank"),
       " or contact ",
       a(href = "mailto:steverozen@pm.me", "steverozen@pm.me",
         target = "_blank")),
    
    # Impressionistic collage
    img(src = "www/rozen-mut-sig-collage.png", 
        width = "500", height = "370"),
    
    # Add a link to the PCAWG7 paper about mutational signatures
    h4("For background see ",
       a(href = "https://doi.org/10.1038/s41586-020-1943-3",
         "\"The repertoire of mutational signatures in human cancer\"", target = "_blank"),
       " and ", a(href = "https://cancer.sanger.ac.uk/cosmic/signatures",
                  "COSMIC Mutational Signatures", target = "_blank"))
    
    
  )
}

#' @import shiny
UploadVCFUI <- function() {
  fluidPage(
    sidebarLayout(
      
      sidebarPanel = sidebarPanel(
        fluidRow(
          column(6, AddReferenceGenome()),
          
          column(6, AddRegionForVCF())
        ),
        
        fluidRow(
          column(6, AddVariantCaller()),
          
          # Hidden at first, pops up if Variant caller is "other"
          column(6, conditionalPanel(
            condition = "input.variantCaller == 'unknown'",
            MergeSBSsAsDBSOption()))),
        fluidRow(
          column(6, UploadVCFFiles()),
          column(
            6, 
            uiOutput(outputId = "clickToCreateCatalogs"),
            br(),
            uiOutput(outputId = "downloadZipFile"),
            br(),
            uiOutput(outputId = "showSpectraFromVCF"),
            br(),
            uiOutput(outputId = "sigAttributionFromVCF"))
        ), width = 5), # end sidbarPanel
      
      mainPanel = mainPanel(
        # Add the next row of control widgets
        fluidRow(
          # Add text input for user to specify the sample names
          # representing different VCF files
          column(6, AddSampleNames()),
        ),
        
        br(),
        # Add a download button for user to download VCF files to test
        fluidRow(column(8,
                        wellPanel(
                          h5(strong("Example data and analysis", style = "color: #337ab7")),
                          br(),
                          
                          downloadButton(outputId = "downloadsampleVCFs",
                                         label = "Download example VCFs"),
                          rep_br(2),
                          
                          actionButton(inputId = "runStrelkaVCFs", 
                                       label = paste0("Example analysis on  ",
                                                      "Strelka VCFs")),
                          
                          rep_br(2),
                          actionButton(inputId = "runMutectVCFs",
                                       label = paste0("Example analysis on ",
                                                      "Mutect VCFs")),
                          rep_br(1))
        ) # end of column
        ), width = 6) # end of mainPanel
    ) # end of sidebarLayout
  )
}

#' @import shiny
golem_add_external_resources <- function(){
  addResourcePath(prefix = "www", directoryPath = 
                    system.file("app/www", package = "mSigAct.server"))
  
  addResourcePath(prefix = "ID", directoryPath = 
                    system.file("app/ID", package = "mSigAct.server"))
  tags$head(
    golem::activate_js(),
    # Add here all the external resources
    # If you have a custom.css in the inst/app/www
    # Or for example, you can add shinyalert::useShinyalert() here
    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
    
    #includeCSS(path = "inst/app/www/style.css")
    
    # Add padding because navbar pinned at the top
    tags$style(type="text/css", "body {padding-top: 75px;}"),
    
    tags$style(
      HTML(".shiny-notification {
              height: 100px;
              width: 800px;
              position:fixed;
              top: calc(50% - 50px);;
              left: calc(50% - 400px);;
            }
           ")),
    
    includeScript("inst/app/www/test.js"),
    includeHTML("inst/app/www/test.html")
  )
}
#' @import shiny
app_ui <- function(request) {
  tagList(
    # Leave this function for adding external resources
    golem_add_external_resources(),
    
    navbarPage(title = tags$b("mSigAct"), id = "panels",
               tabPanel(title = tags$b("Home"), 
                        HomeUI()),
               tabPanel(title = tags$b("Generate spectrum", 
                                       tags$br(), "catalogs from VCFs"),
                        UploadVCFUI(), 
                        value = "generateCatalogTab"),
               tabPanel(title = tags$b("Upload spectra for", tags$br(),
                                       "signature attribution"), 
                        UploadSpectraUI(), 
                        value = "uploadSpectraTab"),
               tabPanel(title = tags$b("Guides", tags$br(), 
                                       "(help)"), 
                        TutorialUI(),
                        value = "tutorialTab"),
               position = "fixed-top",
               windowTitle = "mSigAct: Mutational Signature Activity")
  )
}

#' @import shiny
TutorialUI <- function() {
  #general.guide.path <- system.file("tutorial/top.help.md", 
  #                                  package = "mSigAct.server")
  fluidPage(
    tabsetPanel(
      id = "helpPages", 
      tabPanel(title = tags$b("General guide"),
               includeMarkdown(path = "inst/guides/general.guide.md")),
      tabPanel(title = tags$b("Guide to generating catalogs"),
               includeMarkdown(
                 path = "inst/guides/Guide.to.generating.catalogs.md")),
      tabPanel(title = tags$b("Guide to signature attribution"),
               includeMarkdown(
                 path = "inst/guides/Guide.to.signature.attribution.md"))
    ) # tabsetPanel
  ) # fluidPage
}

#' @import shiny
AttributionResultsUI <- function() {
  fluidPage(
    br(),
    fluidRow(splitLayout(cellWidths = c("25%", "25%", "17.5%", "20%"),
                         actionButton(inputId = "analyzeMoreSample", 
                                      label = "Do another signature attribution",
                                      style = "color: #fff; background-color: #337ab7;
                             border-color: #2e6da4;"),
                         downloadButton(outputId = "downloadExposureTable", 
                                        label = "Download exposure counts"),
                         downloadButton(outputId = "downloadPdf",
                                        label = "Download PDF"),
                         downloadButton(outputId = "downloadMAPTable",
                                        label = "Download diagnostics"))),
    br(),
    DT::dataTableOutput(outputId = "exposureTable"),
    
  )
}

#' @import shiny
HomeUI <- function() {
  # List the first level UI elements here
  fluidPage(
    # Add a title on top the page
    titlePanel(title = p("mSigAct: Mutational Signature Activity",
                         style = "color: #337ab7"),
               windowTitle = paste0("mSigAct: Mutational Signature Activity")),
    
    
    # Add one line break
    # br(),
    
    # Add a short description of msigact
    h4("This web site has two main functions:"),
    
    h4(tags$ol(
      tags$li(actionLink(
        inputId = "linkToGenerateCatalogTab",
        label = "Generate mutational spectrum catalogs from VCFs* and plot them")),
      br(),
      tags$li(actionLink(
        inputId = "linkToUploadSpectraTab",
        label = paste0("Signature attribution: ", 
                       "Estimate which mutational signatures contributed to a ",
                       "mutational spectrum"))),
    )),
    
    h4(a(href = "https://tinyurl.com/rdzwnxd", "*VCFs", target = "_blank"),
       " are file that contain one mutation per line, and are created ",
       "by variant callers such as ",
       a(href = "https://github.com/Illumina/strelka", "Strelka", target = "_blank"), 
       " or ",
       a(href = "https://github.com/broadgsa/gatk", "Mutect", target = "_blank")),
    
    hr(),
    h4("mSigAct webserver can be freely accessed at ", 
       a(href = "https://msigact.ai",
         "https://msigact.ai", target = "_blank")),
    
    h4("To report issues, make suggestions, and request help, ",
       "post on ",
       a(href = "https://github.com/steverozen/mSigAct.server/issues",
         "GitHub", target = "_blank"),
       " or contact ",
       a(href = "mailto:steverozen@gmail.com", "steverozen@gmail.com",
         target = "_blank")),
    
    # Impressionistic collage
    img(src = "www/rozen-mut-sig-collage.png", 
        width = "500", height = "370"),
    
    # Add a link to the PCAWG7 paper about mutational signatures
    h4("For background see ",
       a(href = "https://doi.org/10.1038/s41586-020-1943-3",
         "\"The repertoire of mutational signatures in human cancer\"", target = "_blank"),
       " and ", a(href = "https://cancer.sanger.ac.uk/cosmic/signatures",
                  "COSMIC Mutational Signatures", target = "_blank"))
    
    
  )
}

#' @import shiny
UploadVCFUI <- function() {
  fluidPage(
    sidebarLayout(
      
      sidebarPanel = sidebarPanel(
        fluidRow(
          column(6, AddReferenceGenome()),
          
          column(6, AddRegionForVCF())
        ),
        
        fluidRow(
          column(6, AddVariantCaller()),
          
          # Hidden at first, pops up if Variant caller is "other"
          column(6, conditionalPanel(
            condition = "input.variantCaller == 'unknown'",
            MergeSBSsAsDBSOption(),
            AddFilterStatus()))),
        
        fluidRow(
          column(6, UploadVCFFiles()),
          column(
            6, 
            uiOutput(outputId = "clickToCreateCatalogs"),
            br(),
            uiOutput(outputId = "downloadZipFile"),
            br(),
            uiOutput(outputId = "showSpectraFromVCF"),
            br(),
            uiOutput(outputId = "sigAttributionFromVCF"))
        ), width = 5), # end sidbarPanel
      
      mainPanel = mainPanel(
        # Add the next row of control widgets
        fluidRow(
          # Add text input for user to specify the sample names
          # representing different VCF files
          column(6, AddSampleNames()),
        ),
        
        br(),
        # Add a download button for user to download VCF files to test
        fluidRow(column(8,
                        wellPanel(
                          h5(strong("Example data and analysis", style = "color: #337ab7")),
                          br(),
                          
                          downloadButton(outputId = "downloadsampleVCFs",
                                         label = "Download example VCFs"),
                          rep_br(2),
                          
                          actionButton(inputId = "runStrelkaVCFs", 
                                       label = paste0("Example analysis on  ",
                                                      "Strelka VCFs")),
                          
                          rep_br(2),
                          actionButton(inputId = "runMutectVCFs",
                                       label = paste0("Example analysis on ",
                                                      "Mutect VCFs")),
                          rep_br(1))
        ) # end of column
        ), width = 6) # end of mainPanel
    ) # end of sidebarLayout
  )
}

#' @import shiny
golem_add_external_resources <- function(){
  addResourcePath(prefix = "www", directoryPath = 
                    system.file("app/www", package = "mSigAct.server"))
  
  addResourcePath(prefix = "ID", directoryPath = 
                    system.file("app/ID", package = "mSigAct.server"))
  tags$head(
    golem::activate_js(),
    # Add here all the external resources
    # If you have a custom.css in the inst/app/www
    # Or for example, you can add shinyalert::useShinyalert() here
    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
    
    #includeCSS(path = "inst/app/www/style.css")
    
    # Add padding because navbar pinned at the top
    tags$style(type="text/css", "body {padding-top: 75px;}"),
    
    tags$style(
      HTML(".shiny-notification {
              height: 100px;
              width: 800px;
              position:fixed;
              top: calc(50% - 50px);;
              left: calc(50% - 400px);;
            }
           ")),
    
    includeScript("inst/app/www/test.js"),
    includeHTML("inst/app/www/test.html")
  )
}