R/UI_home_app.R

In Coayala/MetaboTandem: Pipeline for the analysis of LC-MS/MS data

app_header <- function(home = FALSE){
  dashboardHeader(
    title = tagList(
      # TODO logo is not showing
      span(class = "logo-lg", "MetaboTandem"),
      img(src = "logo.png")),

    # Notification menu for adding Github and User guide link
    dropdownMenu(
      type = 'notifications',
      icon = icon('question-circle'),
      headerText = 'Help',

      notificationItem('Github Repository',
                       icon = icon('github'),
                       href = 'https://github.com/Coayala/MetaboTandem'),
      notificationItem('User Guide',
                       icon = icon('file'),
                       href = 'https://github.com/Coayala/MetaboTandem')
    ),
    leftUi = tagList(
      if(home){
        h4('Welcome to MetaboTandem', style = "color:white")
      } else {
        h4()
      }

    )
  )
}


#' Homepage UI
#'
#' UI for displaying MetaboTandem Homepage
home_ui <- dashboardPage(
  #md = TRUE,

  app_header(home = TRUE),

  # Sidebar content
  dashboardSidebar(),

  # Body content
  dashboardBody(
    fluidRow(
      # Box for Autotuner
      box(title = 'Estimate Parameters',
          headerBorder = FALSE,
          background = 'purple',
          collapsible = FALSE,
          closable = FALSE,
          gradient = TRUE,
          footer = p('Use Autotuner to estimate the best parameters for your run',
                     style = 'color:gray'),
          fluidRow(
            column(6, align = 'center', offset = 3,
                   shinyWidgets::actionBttn(inputId = 'goAutotuner',
                                            icon = icon('lightbulb'),
                                            style = 'jelly',
                                            size = 'lg'))
          )
      ),

      # Box for the main pipeline
      box(title = 'Full Data analysis',
          headerBorder = FALSE,
          background = 'light-blue',
          collapsible = FALSE,
          closable = FALSE,
          gradient = TRUE,
          footer = p('Run the full analysis starting from mas spectra data',
                     style = 'color:gray'),
          fluidRow(
            column(6, align = 'center', offset = 3,
                   shinyWidgets::actionBttn(inputId = 'goMain',
                                            icon = icon('chart-simple'),
                                            style = 'jelly',
                                            size = 'lg'))
          )
      ),

      # Box for manage databases
      box(title = 'Manage Databases',
          headerBorder = FALSE,
          background = 'olive',
          collapsible = FALSE,
          closable = FALSE,
          gradient = TRUE,
          footer = p('Create custom database or download public databases',
                     style = 'color:gray'),
          fluidRow(
            column(6, align = 'center', offset = 3,
                   shinyWidgets::actionBttn(inputId = 'goDatabase',
                                            icon = icon('database'),
                                            color = 'default',
                                            style = 'jelly',
                                            size = 'lg'))
            #this is were box is made active to go to database
          )
      ),

      # Box for the annotate MGF
      box(title = 'Annotate MGF',
          headerBorder = FALSE,
          background = 'maroon',
          collapsible = FALSE,
          closable = FALSE,
          gradient = TRUE,
          footer = p('Annotate MS2 spectra using custom or public databases',
                     style = 'color:gray'),
          fluidRow(
            column(6, align = 'center', offset = 3,
                   shinyWidgets::actionBttn(inputId = 'goAnnotate',
                                            icon = icon('magnifying-glass'),
                                            style = 'jelly',
                                            size = 'lg'))
          )
      )
    )
  )
)