R/feature_input_module.R

In microbiomeExplorer: Microbiome Exploration App

#' Main feature analysis input module.
#' Set up to handle all analysis tabs in the app depending on given parameters
#'
#' @param id element identifier - namespace
#'
#' @author Janina Reeder
#'
#' @return box containing ui element
featureInputUI <- function(id) {
    ns <- NS(id)

    box(width = 12, id = ns("analysisbox"),
        h4("ANALYSIS PARAMETERS"),

        div(
          selectInput(ns("facetby"),
                      label = "Facet columns by", choices = "", 
                      multiple = FALSE, 
                      selectize = FALSE, width = "250px"
          ),
          selectInput(ns("facetby2"),
                      label = "Facet rows by", choices = "", 
                      multiple = FALSE, 
                      selectize = FALSE, width = "250px"
          )
        ),
        ## buttons are used to submit events. This ensures plots are not redrawn 
        ## while user still adjusts parameters
        div(id = ns("buttondiv"),
            fluidRow( width = 12, id = "actionbuttonrow",
                ## update analysis outputs (plots/tables)
                actionButton(ns("updatebutton"), 
                             icon = icon("far fa-chart-bar"),
                             label = HTML("&nbsp;UPDATE"), 
                             width = "120px"),
                actionButton(ns("reportButton"), 
                             label = HTML("<i class='far fa-bookmark'></i>&nbsp;&nbsp;REPORT"), 
                             width = "120px")
            )
        )
    )
}


#' Server side for the feature analysis input module
#'
#' @param input shiny input
#' @param output shiny output
#' @param session shiny session
#' @param meData MRExperiment object storing all data
#' @param facetOptions named vector of available facet choices
#' @param reset reactive boolean determining if all inputs should be reset 
#' @param aggDat aggregated MRExperiment object (default is NULL)
#'
#' @author Janina Reeder
#' 
#' @importFrom metagenomeSeq MRcounts
#' @importFrom Biobase pData fData
#'
#' @return list holding all chosen values and the selected feature
featureInput <- function(input, output, session, 
                          meData, facetOptions = NULL, 
                          reset, aggDat = reactive(NULL)) {
    ns <- session$ns

    ## reactive value storing choices made in the UI
    chosenValues <- reactiveVal(NULL)
    ## reactive storing sorted features at given level
    aggFeatures <- reactiveVal(NULL)

    observe({
        req(aggDat())
        aggFeatures(rownames(MRcounts(aggDat())))
        shinyjs::enable("savebutton")
    })

    ## reset all entries
    observe({
        req(reset())
        chosenValues(NULL)
        aggFeatures(NULL)
        shinyjs::disable("savebutton")
    })

    
    ## initialize input elements
    observe({
      req(meData())
      updateSelectInput(session, "facetby", 
                        choices = c("", facetOptions()), 
                        selected = chosenValues()$facetby)
      updateSelectInput(session, "facetby2", 
                        choices = c("", facetOptions()), 
                        selected = chosenValues()$facetby2)
    })

    ## react to first facet variable (phenotype variables should be distinct)
    observeEvent(input$facetby, {
      req(facetOptions())
      facetopts <- facetOptions()
      facetopts <- facetopts[!facetopts %in% input$facetby]
      updateSelectInput(session, "facetby2", choices = c("", facetopts), 
                        selected = input$facetby2)
    }, priority = 15, ignoreInit = TRUE)
    
    ## react to second facet variable (phenotype variables should be distinct)
    observeEvent(input$facetby2, {
      req(facetOptions())
      facetopts <- facetOptions()
      facetopts <- facetopts[!facetopts %in% input$facetby2]
      updateSelectInput(session, "facetby", choices = c("", facetopts), 
                        selected = input$facetby)
    }, priority = 15, ignoreInit = TRUE)


    
    ## main control button: store input choices in chosenValues
    observeEvent(input$updatebutton, {
      facet1 <- NULL
      if(!is.null(input$facetby)){
        if(input$facetby != "")
          facet1 <- input$facetby
      }
      facet2 <- NULL
      if(!is.null(input$facetby2)){
        if(input$facetby2 != "")
          facet2 <- input$facetby2
      }
      cV <- list("facetby" = facet1,
                 "facetby2" = facet2)
      chosenValues(cV)
    })
    

    return(list(chosenValues = chosenValues))
}