R/app_ui.R

In PERK: Predicting Environmental Concentration and Risk

#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#'     DO NOT REMOVE.
#' @importFrom bs4Dash bs4DashPage dashboardHeader bs4DashSidebar sidebarUserPanel bs4DashBrand bs4SidebarMenu bs4SidebarMenuItem bs4SidebarMenuSubItem bs4DashBody bs4TabItem bs4TabItems box bs4DashControlbar controlbarMenu controlbarItem skinSelector
#' @importFrom colourpicker colourInput
#' @importFrom shinyWidgets sliderTextInput
#' @importFrom shiny fluidRow selectInput tagList tags icon tabPanel sidebarPanel mainPanel h4 p br
#'
#' @noRd
app_ui <- function(request) {
  shiny::tagList(
    # Leave this function for adding external resources
    golem_add_external_resources(),

    # Your application UI logic
    bs4Dash::bs4DashPage(
      #dark = TRUE,
      help = FALSE,
      fullscreen = TRUE,
      scrollToTop = TRUE,

      # Header
      header = bs4Dash::dashboardHeader(
        title = bs4Dash::bs4DashBrand(
          title = "PERK",
          opacity = 0.8),
        fixed = TRUE,
        controlbarIcon = shiny::icon("tools")
),

sidebar = bs4Dash::bs4DashSidebar(
        fixed = TRUE,
        skin = "light",
        status = "primary",
        id = "sidebar",
        bs4Dash::sidebarUserPanel(
          name = "Welcome Onboard!"
        ),
        bs4Dash::bs4SidebarMenu (
          id = "current_tab",
          flat = FALSE,
          compact = FALSE,
          childIndent = TRUE,
          shiny::tags$hr(),
          bs4Dash::bs4SidebarMenuItem("Info",
                                      bs4Dash::bs4SidebarMenuSubItem("About", tabName = "about_info"),
                                      icon =shiny::icon("circle-info")),
          bs4Dash::bs4SidebarMenuItem("Upload Data",
                            tabName = "user_input",
                            icon =shiny::icon("upload")),
          bs4Dash::bs4SidebarMenuItem("Predicted",
                            icon =shiny::icon("long-arrow-alt-left"),
                           bs4Dash::bs4SidebarMenuSubItem("Prescription", tabName = "pec_12"),
                           bs4Dash::bs4SidebarMenuSubItem("Predicted Concentrations", tabName = "pec_11")
          ),
          bs4Dash::bs4SidebarMenuItem("Measured",
                            tabName = "mec_11",
                            icon =shiny::icon("long-arrow-alt-right")),
          bs4Dash::bs4SidebarMenuItem("Predicted v Measured",
                   icon =shiny::icon("exchange-alt"),
                   bs4Dash::bs4SidebarMenuSubItem ("Predicted Vs Measured", tabName = "pcvsmc_11"),
                   bs4Dash::menuSubItem("Prediction Accuracy", tabName = "pcvsmc_12")
          ),

          shiny::tags$hr()

        )
      ), # Close of sidebar
body = bs4Dash::bs4DashBody(
#body = bs4Dash::dashboardBody(
        bs4Dash::bs4TabItems(
          bs4Dash::bs4TabItem(
            tabName = "about_info",
            shiny::tabPanel("About", value = "about",
                     shiny::sidebarPanel(width=1),
                     shiny::mainPanel(width=8,
                               shiny::h4("About:"),
                              shiny::p("PERK: An in-built application to predict and visualize environmental concentration and risk using pharmaceutical prescription data collected at fine spatial resolution."
                               ),
                              shiny::p("PERK acronym for Predicting Environmental concentrations and RisK assessment, is an R package with in-built application tool, aims to facilitate automated modelling and reporting of predicted environmental concentrations of a comprehensive set of pharmaceuticals derived from a wide range of therapeutic classes with different mode of action."),
                              shiny::p("The tool helps users,",
                                 shiny::tags$li("to input their measured concentration,"),
                                 shiny::tags$li("to compare the predicted and measured concentrations of the APIs by means of the PEC/MEC ratio, "),
                                 shiny::tags$li("to establish whether the predicted equations used tend to underestimate or overestimate measured values."),
                                 shiny::tags$li("It provides a consistent interactive user interface in a familiar dashboard layout, enabling users to visualise predicted values and compare with their measured values without any hassles."),
                                 shiny::tags$li("Users can download data and graphs generated using the tool in .csv or publication ready images (.pdf, .eps).")
                               ),
                               shiny::h4("Acknowledgments:"),
                              shiny::p("This work is a part of the Wastewater Fingerprinting for Public Health Assessment (ENTRUST) project funded by Wessex Water and EPSRC IAA (grant no. EP/R51164X/1)."),
                              shiny::br()
                     )
            )
          ),
          bs4Dash::bs4TabItem(
            tabName = "user_input",
            shiny::fluidRow(
              bs4Dash::box(
                title = "Pharmaceuticals Data",
                width = 4,
                closable = FALSE,
                collapsible = TRUE,
                maximizable = TRUE,
                mod_user_input_ui("user_input_1", "Pharmaceuticals list (PL)"),
                mod_user_input_ui("user_input_2", "Prescription Data (Rx)"),
                mod_user_input_ui("user_input_3", "API Data"),
                mod_user_input_ui("user_input_6", "Metabolism Data (Fx)"),
                mod_user_input_ui("user_input_7", "Measured Data (MC)")
              ),
              bs4Dash::box(
                title = "WWTP Data",
                width = 4,
                closable = FALSE,
                collapsible = TRUE,
                maximizable = TRUE,
                mod_user_input_ui("user_input_8", "Flow Data (FL)"),
                mod_user_input_ui("user_input_4", "WWTP Site Info (SI)"),
                mod_user_input_ui("user_input_5", "Removal Efficiency (RE)")
              ),
              bs4Dash::box(
                title = "Environmental Data",
                width = 4,
                closable = FALSE,
                collapsible = TRUE,
                maximizable = TRUE
              )
            )
            ),
          bs4Dash::bs4TabItem (
            tabName = "pec_12",
            mod_presc_dash_ui("presc_dash_1")
          ),
          bs4Dash::bs4TabItem (
            tabName = "pec_11",
            mod_pec_dash_ui("pec_dash_1")
          ),
          bs4Dash::bs4TabItem (
            tabName = "mec_11",
            mod_mec_dash_ui("mec_dash_1")
          ),
          bs4Dash::bs4TabItem (
            tabName = "pcvsmc_11",
            mod_pecvsmec_dash_ui("pecvsmec_dash_1")
          ),
          bs4Dash::bs4TabItem (
            tabName = "pcvsmc_12",
            mod_predacc_dash_ui("predacc_dash_1")
          )
        )# End of bs4TabItems
      ), #close of body

controlbar =  bs4Dash::bs4DashControlbar (
        id = "controlbar",
        skin = "light",
        pinned = FALSE,
        overlay = FALSE,
        width = 400,
        bs4Dash::controlbarMenu(
          id = "controlbarMenu",
          type = "pills",
          bs4Dash::controlbarItem(
            "Skin",
            #icon =  "fa-solid fa-palette",
            bs4Dash::skinSelector()
          ),
          bs4Dash::controlbarItem(
            "Plot",
            shiny::selectInput('plot_colors',
                               'Plot Fill Colours:',
                               c(
                                 'default' = 'viridis',
                                 'Grey' = 'Greys',
                                 'YlOrRd' = 'YlOrRd',
                                 'Pastel1' = 'Pastel1',
                                 'Pastel2' = 'Pastel2',
                                 'Dark2' = 'Dark2',
                                 'Accent' = 'Accent'),
                               selected = 'default'),
            shinyWidgets::sliderTextInput(
              inputId = "widthPlotOutline",
              label = "Plot width:",
              choices = seq(from = 0,
                            to = 5,
                            by = 0.25),
              grid = TRUE
            ),
            shinyWidgets::sliderTextInput(
              inputId = "geomTextDodgeY",
              label = "Text Y (points):",
              choices = seq(from = 0,
                            to = 2,
                            by = 0.1),
              grid = TRUE
            ),
            shinyWidgets::sliderTextInput(
              inputId = "geomTextDodgeX",
              label = "Text X (points):",
              choices = seq(from = 0,
                            to = 2,
                            by = 0.1),
              grid = TRUE
            ),
            colourpicker::colourInput("colPlotOutline",
                                      "Points outline",
                                      "black", allowTransparent = TRUE)

          )
        )
      )
    )
  )
}

#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @importFrom shiny tags
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function() {
  add_resource_path(
    "www",
    app_sys("app/www")
  )

  shiny::tags$head(
    favicon(),
    bundle_resources(
      path = app_sys("app/www"),
      app_title = "PERK"
    )
    # Add here other external resources
    # for example, you can add shinyalert::useShinyalert()
  )
}