R/mod_dashboard_structure.R

In Fjeanneret/multiSight: Multi-omics Classification, Functional Enrichment and Network Inference analysis

#' dashboard_structure UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd 
#'
#' @importFrom shiny NS tagList column sliderInput
#' textInput actionButton htmlOutput fluidRow icon h1
#' @import shinydashboard  
mod_dashboard_structure_ui <- function(id){
  ns <- NS(id)
  dashboardPage(
    dashboardHeader(title = "multiSight"),
    
    dashboardSidebar(    
      sidebarMenu(
        menuItem("Home", 
                 tabName = "home", 
                 icon = icon("home")),
        menuItem("Classification", 
                 tabName = "models", 
                 icon = icon("bullseye")),
        menuItem("Biological Insights",
                 tabName = "understand", 
                 icon = icon("database")),
        menuItem("Assumptions", 
                 tabName = "hypothesis", 
                 icon = icon("book"))
      )),
    
    dashboardBody(
      fluidRow(
        tabItems(
          # Home tab content
          tabItem(
            box(title = h1(icon("seeding"), "Welcome to multiSight!"),
                width = 10, status = "warning",
                  "This Home tab is dedicated to input omic datasets and 
                    to save results.",br(),
                  "Every omic data as numeric matrices could be used here.", 
                  br(),
                  "Please, provide data sets as data.frame for omic data and 
                  classes vector where rows are sample's names and columns 
                  biological features (e.g. genes, proteins expressions)."
            ),
            # h1("Home", align = "center"), 
            tabName = "home",
            # mod_home_ui("home_ui_1")
            mod_user_input_ui("user_input_ui_1")
          ),
          # Discrimination tab content
          tabItem(
            box(title = h1("Classification"),
                width = 10, status = "warning",
                "This Classification tab is dedicated to classification models
                performances and selected features by Biosigner and Diablo.",
                br(),
                "Detailed features tables are provided with means of each 
                feature for each class and DESEQ2 information when computed."
            ),
            tabName = "models",
            mod_MLmodels_ui("MLmodels_ui_1")
          ),
          # Understand tab content
          tabItem(
            box(title = h1("Biological Insights"),
                width = 10, status = "warning",
                "This Biological Insights tab is dedicated to single-omic and 
                multi-omic functional enrichment with diablo or DESeq2 
                selected features.", br(), " In case of 2 or more omic datasets 
                enriched, Stouffer's values and relative enrichment map for 
                each pathways or ontology are provided to see at a glance which
                ones are meaningful between several omics data.
                "
            ),
            tabName = "understand", 
            mod_understand_ui("understand_ui_1")
          ),
          # Hypothesis tab content
          tabItem(
            box(title = h1("Assumptions"),
                width = 10, status = "warning",
                "This Assumptions tab is dedicated to Network inferences and 
                a integrated PubMed query module.", br(),
                "Networks are build according to 3 methods: correlation, 
                partial correlation and mutual information (see ", 
                tags$a(href="https://doi.org/10.3389/fgene.2019.00535", 
                       "Inferring Interaction Networks From Multi-Omics Data", 
                       target="_blank"), ")."
                
            ),
                  
              tabName = "hypothesis", 
              box(title ="Diablo features", width = 10, 
                  status = "warning", collapsible = TRUE,
                  solidHeader = TRUE, 
                  actionButton(ns("diabloNetworkStart"),
                         "Build networks", icon("project-diagram")),
                  rep_br(times = 2),
                  mod_hypothesisGenerator_ui(ns("hypothesisGenerator_ui_1"))
            ),
            box(title ="Biosigner features", width = 10, 
                status = "warning", collapsible = TRUE,
                solidHeader = TRUE,
                actionButton(ns("biosignerNetworkStart"),
                         "Build networks", icon("project-diagram")),
                rep_br(times = 2),
                mod_hypothesisGenerator_ui(ns("hypothesisGenerator_ui_2"))
          )
        )
      )
    )
  )
)
}
    
#' dashboard_structure Server Function
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#' @param obj R6 object to wrap all data from different analysis.
#'
#' @importFrom shiny observeEvent req 
#'
#' @noRd 
mod_dashboard_structure_server <- function(input,
                                           output, 
                                           session)
{
  
    obj <- obj
    ns <- session$ns
    observeEvent(input$diabloNetworkStart,{
      req(length(obj$classification$diabloResult$biosignature) > 0)
      biosignature <- obj$classification$diabloResult$biosignature
      callModule(mod_hypothesisGenerator_server, 
                 "hypothesisGenerator_ui_1", 
                 obj, 
                 biosignature,
                 "diabloNetwork")
    })
    
    observeEvent(input$biosignerNetworkStart, {
      req(length(obj$classification$biosignerResult$biosignature) > 0)
      biosignature <- obj$classification$biosignerResult$biosignature
      callModule(mod_hypothesisGenerator_server, 
                 "hypothesisGenerator_ui_2", 
                 obj, 
                 biosignature,
                 "biosignerNetwork")
    })
  # callModule(mod_user_input_server, "user_input_ui_1")  
}
    
## To be copied in the UI
# mod_dashboard_structure_ui("dashboard_structure_ui_1")
    
## To be copied in the server
# callModule(mod_dashboard_structure_server, "dashboard_structure_ui_1")