R/run.R

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

#########################################
#### A Shiny App for UCSC Xena ##########
#########################################
##### LICENSE: GPLv3 @Openbiox   ##########
#########################################


#' Run UCSC Xena Shiny App
#'
#' @importFrom shiny shinyAppFile
#' @inheritParams shiny::runApp
#' @param runMode default is 'client' for personal user, set it to 'server' for running on server.
#' @return NULL
#' @export
#'
#' @examples
#' \dontrun{
#' app_run()
#' }
app_run <- function(runMode = "client", port = getOption("shiny.port")) {
  runMode <- match.arg(runMode, choices = c("client", "server"))
  options(xena.runMode = runMode)
  shiny::shinyAppFile(system.file("shinyapp", "App.R", package = "UCSCXenaShiny"),
    options = list(port = port)
  )
}




#' Run UCSC Xena Shiny App with specifc content
#'
#' @importFrom shiny shinyAppFile
#' @inheritParams shiny::runApp
#' @param runMode default is 'client' for personal user, set it to 'server' for running on server.
#' @param content Modules to enable. 
#' - `a`: all modules
#' - `s`: only loading basic modules; 
#' - `q`: add tpc (TCGA, PCAWG, CCLE) modules
#' - `p`: add tpc pipelines
#' - `d`: add pharmcogenomics modules
#'
#' @return NULL
#' @export
#'
#' @examples
#' \dontrun{
#' app_run2(content = "s")
#' }
app_run2 <- function(runMode = "client", port = getOption("shiny.port"),
                     content = c("a", "s", "q", "p", "d")) {
  runMode <- match.arg(runMode, choices = c("client", "server"))
  options(xena.runMode = runMode)
  content <- match.arg(content)
  if (content == "a") {
    cm1 <- ""
    cm2 <- ""
    cm3 <- ""
    cm0 <- ""
    cm_link <- "#"
  } else if (content == "s") {
    cm1 <- "#"
    cm2 <- "#"
    cm3 <- "#"
    cm0 <- ""
    cm_link <- "#"
    if (runMode == "server") {
      cm_link <- ""
    } # server application with link2advanced tabpanel
  } else if (content == "q") {
    cm1 <- ""
    cm2 <- "#"
    cm3 <- "#"
    cm0 <- "#"
    cm_link <- "#"
  } else if (content == "p") {
    cm1 <- "#"
    cm2 <- ""
    cm3 <- "#"
    cm0 <- "#"
    cm_link <- "#"
  } else if (content == "d") {
    cm1 <- "#"
    cm2 <- ""
    cm3 <- ""
    cm0 <- "#"
    cm_link <- "#"
  }
  codes <- glue::glue(
    'source(system.file("shinyapp/app_preset.R", package = "UCSCXenaShiny")) \n',
    "\n",
    "ui <- tagList( \n",
    "  tags$head( \n",
    '    tags$title("XenaShiny"), \n',
    '    # tags$link(rel = "icon", type="image/svg+xml", href = "./icon.svg"), \n',
    '    tags$link(rel = "icon", type="image/png", href = "./icon.png"), \n',
    '    tags$link(rel = "stylesheet", type = "text/css", href = "./css/global.css") \n',
    "  ), \n",
    "  useWaiter(), \n",
    "  waiterPreloader(html = tagList( \n",
    "    spin_fading_circles(), \n",
    "    br(), br(), \n",
    '    h1(strong("Welcome to use UCSCXenaShiny v2 application!")), \n',
    "    br(), \n",
    '    p("An interactive web tool with general and personalized modules to explore UCSC Xena datasets" \n',
    '      ,style = "font-size: 25px;"), \n',
    "    br(),br(), \n",
    '    p("Notes:", "(1) The initiation could take about 10 seconds. (2) Please zoom in or up screen for better representation.", \n',
    '      style = "font-size: 16px;") \n',
    '  ), color = "#2C3E50"), \n',
    "  shinyjs::useShinyjs(), \n",
    "  autoWaiter(html = spin_loader(), color = transparent(0.5)), # change style https://shiny.john-coene.com/waiter/ \n",
    "  navbarPage( \n",
    '    id = "navbar", \n',
    '    title = "UCSCXenaShiny v2", \n',
    '    windowTitle = "UCSCXenaShiny", \n',
    "    # inst/shinyapp/ui \n",
    "    ui.page_home(), \n",
    "    {cm0}ui.page_repository(), \n",
    "    {cm0}ui.page_general_analysis(), \n",
    "    {cm_link}ui.link2advanced(), \n",
    "    {cm1}ui.page_pancan_quick(), \n",
    "    {cm2}ui.page_pancan_tcga(), \n",
    "    {cm3}ui.page_PharmacoGenomics(), \n",
    "    {cm0}ui.page_download(), \n",
    "    ui.page_help(), \n",
    "    ui.page_developers(), \n",
    "    footer = ui.footer(), \n",
    "    collapsible = TRUE, \n",
    '    theme = tryCatch(shinythemes::shinytheme("flatly"), \n',
    "                     error = function(e) {{ \n",
    '                       "Theme \'flatly\' is not available, use default." \n',
    "                       NULL \n",
    "                     }}) \n",
    "  ) \n",
    ") \n",
    "\n",
    "server <- function(input, output, session) {{ \n",
    '  message("Shiny app run successfully! Enjoy it!\n") \n',
    '  message("               --  Xena shiny team\n") \n',
    "  # Stop warn \n",
    '  storeWarn <- getOption("warn") \n',
    "  options(warn = -1) \n",
    "  # observe(print(input$navbar)) \n",
    "  # inst/shinyapp/server \n",
    '  source(server_file("home.R"), local = TRUE) \n',
    '  source(server_file("repository.R"), local = TRUE) \n',
    '  source(server_file("modules.R"), local = TRUE) \n',
    '  source(server_file("general-analysis.R"), local = TRUE) \n',
    '  observe_helpers(help_dir = system.file("shinyapp", "helper", package = "UCSCXenaShiny")) \n',
    "}} \n",
    "\n",
    "shiny::shinyApp( \n",
    "  ui = ui, \n",
    "  server = server \n",
    ") \n"
  )


  app_file <- paste0(get_cache_dir(), "/App_", content, ".R")
  dirname(app_file)

  if (!dir.exists(dirname(app_file))) {
    dir.create(dirname(app_file), recursive = TRUE)
  }

  readr::write_file(codes, file = app_file)

  shiny::shinyAppFile(app_file,
    options = list(port = port)
  )
}