R/app_ui.R

In erifa1/ExploreMetabar: ExploreMetabar

#' @import shiny
#' @import shinydashboard
#' @import shinyWidgets
#' @importFrom base64enc dataURI


SK8img <- base64enc::dataURI(file=system.file(file.path('app/www', 'SK8.png'), package='ExploreMetabar'))
UCAimg <- base64enc::dataURI(file=system.file(file.path('app/www', 'uca2.png'), package='ExploreMetabar'))
MIGimg <- base64enc::dataURI(file=system.file(file.path('app/www', 'migale2.png'), package='ExploreMetabar'))

app_ui <- function() {
  tagList(
    # Leave this function for adding external resources
    golem_add_external_resources(),
    # shinyjs::useShinyjs(), # used for onclick function from shinyjs package.
    # List the first level UI elements here
    dashboardPage(skin = "red",
                  dashboardHeader(
                      title = "Explore Metabar",

                      tags$li(class="dropdown",tags$a("Hosted by", img(src = SK8img,
                      title = "SK8", height = "20px"), headerText = "Source code",href="https://sk8.inrae.fr/", target="_blank")),

                      tags$li(class="dropdown",tags$a(img(src = UCAimg,
                      title = "UCA", height = "20px"), headerText = "Source code",href="https://mesocentre.uca.fr/", target="_blank")),

                      tags$li(class="dropdown",tags$a(img(src = MIGimg,
                      title = "Migale", height = "20px"), headerText = "Source code",href="https://migale.inrae.fr/", target="_blank")),


                      tags$li(class="dropdown",tags$a(icon("gitlab"), headerText = "Source code",href="https://forgemia.inra.fr/umrf/exploremetabar", target="_blank")),
                      tags$li(class="dropdown",tags$a(icon("clinic-medical"), headerText = "Issues",href="https://forgemia.inra.fr/umrf/exploremetabar/-/issues", target="_blank")),
                      tags$li(class="dropdown",tags$a(icon("twitter"), headerText = "Share", href="
https://twitter.com/intent/tweet?text=ExploreMetabar%3A%20a%20shiny%20application%20to%20explore%20amplicon%20targeted%20metagenomic%20data.%20%23inrae%20%23microbiome%20%23amplicon&url=https%3A%2F%2Fforgemia.inra.fr%2Fumrf%2Fexploremetabar", target="_blank"))
                                  ),


                  dashboardSidebar(
                    sidebarMenu(
                      id="tabs",
                      style = "position: fixed; overflow: visible",
                      menuItem("Input Data", tabName= 'data_loading', icon=icon("diagnoses")),
                      menuItem("Community Composition", tabName = "tab_compo", icon = icon("chart-pie")),
                      menuItem("Alpha diversity", tabName = "tab_alpha", icon = icon("chart-bar")),
                      menuItem("Beta diversity ", tabName = "tab_beta", icon = icon("chart-bar")),
                      menuItem("Boxplot/Tests", tabName = "tab_boxplot", icon = icon("microscope")),
                      menuItem('Heatmap', tabName = 'heatmap', icon = icon('chart-bar')),
                      menuItem("Differential Analysis", tabName = "tab_diff", icon = icon("microscope")),
                      menuItem("ASVenn", tabName = "tab_asvenn", icon = icon("microscope")),
                      menuItem("SourceTracker", tabName = "source_tracker", icon = icon("sourcetree"))

                      # menuItem("PLN network", tabName = "tab_networkpln", icon = icon("project-diagram")),
                      # menuItem("DiffExplore", tabName = "tab_diffexplore", icon = icon("leaf"))
                    )
                  ),

                  dashboardBody(
                    tags$head(includeCSS(system.file(file.path('app/www', 'style.css'), package='ExploreMetabar'))),
                    tabItems(
                      tabItem(tabName = 'data_loading',
                              mod_data_loading_ui("data_loading_ui_1")
                      ),
                      tabItem(tabName = "tab_compo",
                              mod_compo_ui("compo_ui_1")
                      ),
                      tabItem(tabName = "tab_alpha",
                              mod_alpha_ui("alpha_ui_1")
                      ),
                      tabItem(tabName = "tab_beta",
                              mod_beta_ui("beta_ui_1")
                      ),
                      tabItem(tabName = "tab_boxplot",
                              mod_taxaboxplot_ui("taxaboxplot_ui_1")
                      ),
                      tabItem(tabName = "tab_diff",
                              mod_diffanalysis_ui("diffanalysis_ui_1")
                      ),
                      tabItem(tabName = "tab_asvenn",
                              mod_asvenn_ui("asvenn_ui_1")
                      ),
                      tabItem(tabName = "source_tracker",
                              mod_source_tracker_ui("source_tracker_ui_1")
                      ),
                      tabItem(tabName = "heatmap",
                              mod_heatmap_ui("heatmap_ui_1")
                      )#,
                      # tabItem(tabName = "tab_networkpln",
                      #         mod_networkpln_ui("networkpln_ui_1")
                      # ),
                      # tabItem(tabName = "tab_diffexplore",
                      #         mod_diffexplore_ui("diffexplore_ui_1")
                      # )
                    )
                  )

    )

  )
}

#' @import shiny
golem_add_external_resources <- function(){

  addResourcePath(
    'www', system.file('app/www', package = 'ExploreMetabar')
  )

  tags$head(
    golem::activate_js(),
    golem::favicon()
    # Add here all the external resources
    # If you have a custom.css in the inst/app/www
    # Or for example, you can add shinyalert::useShinyalert() here
    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
  )
}