R/Module_columnSelModule.R

In mjhelf/Mosaic: Metaboseek platform

#' ColumnSelModule
#' 
#' server module for selection of columns to show in main Table
#' 
#' @inherit MseekModules
#' 
#' @import shiny
#' 
#' @describeIn ColumnSelModule server logic for ColumnSelModule
#' @export 
ColumnSelModule <- function(input, output, session,
                            values){
    ns <- NS(session$ns(NULL))
    
    
    internalValues <- reactiveValues(selectedGroup = NULL,
                                     gPropsSelected = NULL,
                                     sPropsSelected = NULL,
                                     intensitiesSelected = NULL,
                                     othersSelected = NULL,
                                     rtMin = F
    )
    
    observeEvent(c(#values$featureTables$active,
        colnames(values$featureTables$tables[[values$featureTables$active]]$df)
    ),{
        
        if( !identical(internalValues$colnames, colnames(values$featureTables$tables[[values$featureTables$active]]$df))){
            
            
            if(!is.null(values$featureTables$tables[[values$featureTables$active]]$gNames) 
               && (is.null(internalValues$selectedGroup)
                   || !internalValues$selectedGroup %in% values$featureTables$tables[[values$featureTables$active]]$gNames)){
                internalValues$selectedGroup <- values$featureTables$tables[[values$featureTables$active]]$gNames[1]
            }
            
            
            internalValues$colnames <- colnames(values$featureTables$tables[[values$featureTables$active]]$df)
            
            values$featureTables <- values$featureTables
            if(!is.null(internalValues$selectedGroup)){
                
                internalValues$gPropsSelected <- values$featureTables$tables[[values$featureTables$active]]$gProps[[internalValues$selectedGroup]]
                
                internalValues$sPropsSelected <- values$featureTables$tables[[values$featureTables$active]]$sProps[[internalValues$selectedGroup]]
                internalValues$intensitiesSelected <- values$featureTables$tables[[values$featureTables$active]]$anagroupnames[[internalValues$selectedGroup]]
            }
        }
        
        
        
        internalValues$othersSelected <- unique(c(internalValues$colnames[internalValues$colnames %in% internalValues$othersSelected],
                                                  values$featureTables$tables[[values$featureTables$active]]$summaryStats))
        
    })
    
    ###Column Selection
    
    output$mainSelGroup <- renderUI({
        tagList(fluidRow(
            checkboxInput(ns("rtMin"), "Show RT in minutes", value = internalValues$rtMin)),
            fluidRow(
                selectizeInput(ns('mainSelGroup'), 'Group of interest',
                               choices = values$featureTables$tables[[values$featureTables$active]]$gNames,
                               selected = internalValues$selectedGroup,
                               multiple = F,
                               width = '100%')
            ))
    })
    
    output$mainSelgProps <- renderUI({selectizeInput(ns('mainSelgProps'), 'Group properties', 
                                                     choices = values$featureTables$tables[[values$featureTables$active]]$gProps,
                                                     selected = internalValues$gPropsSelected,
                                                     multiple = T,
                                                     width = '100%')
    })
    
    observeEvent(c(input$mainSelgProps),
                 {internalValues$gPropsSelected <- input$mainSelgProps })
    
    observeEvent(c(input$rtMin),
                 {
                     if(input$rtMin){
                         values$featureTables$tables[[values$featureTables$active]]$core <- c("mz","rt_minutes","comments","rt")
                     }else{
                         values$featureTables$tables[[values$featureTables$active]]$core <- c("mz","rt","comments")
                     }
                     internalValues$rtMin <- input$rtMin
                 })
    
    
    output$mainSelsProps <- renderUI({
        #print(FeatureTable(values)$sProps)
        selectizeInput(ns('mainSelsProps'), 'Sample properties', 
                                                     choices = values$featureTables$tables[[values$featureTables$active]]$sProps,
                                                     selected = internalValues$sPropsSelected,
                                                     multiple = T,
                                                     width = '100%')})
    
    observeEvent(c(input$mainSelsProps),
                 {internalValues$sPropsSelected <- input$mainSelsProps })
    
    output$mainSelIntensities <- renderUI({
        
        
        # intShowAs <- lapply(values$featureTables$tables[[values$featureTables$active]]$anagroupnames, as.list)
        # singlegroups <- which(lengths(intShowAs) == 1)
        # for (i in singlegroups){
        #     names(intShowAs[[i]]) <- intShowAs[[i]]
        # }
        # 
        # 
        # intNormShowAs <- lapply(values$featureTables$tables[[values$featureTables$active]]$anagroupnames_norm, as.list)
        # singlegroups <- which(sapply(intNormShowAs,length) == 1)
        # for (i in singlegroups){
        #     names(intNormShowAs[[i]]) <- intNormShowAs[[i]]
        # }
        
        
        # print(list(Intensities = intShowAs,
        #            "Normalized Intensities" = intNormShowAs))
        
        selectizeInput(ns('mainSelIntensities'), 'Sample intensities', 
                       choices = c(FeatureTable(values)$anagroupnames, FeatureTable(values)$anagroupnames_norm),
                           # list(Intensities = intShowAs,
                           #            "Normalized Intensities" = intNormShowAs),
                       selected = internalValues$intensitiesSelected,
                       multiple = T,
                       width = '100%')})
    
    observeEvent(c(input$mainSelIntensities),
                 {internalValues$intensitiesSelected <- input$mainSelIntensities })
    
    
    output$mainSelOthers <- renderUI({
        baseStats <- values$featureTables$tables[[values$featureTables$active]]$summaryStats
        names(baseStats) <- values$featureTables$tables[[values$featureTables$active]]$summaryStats
        Others <- values$featureTables$tables[[values$featureTables$active]]$others
        names(Others) <- values$featureTables$tables[[values$featureTables$active]]$others
        
        
        selectizeInput(ns('mainSelOthers'), 'other columns', 
                       choices = list("Basic Stats" = baseStats,
                                      "Others" = Others),
                       selected =  internalValues$othersSelected, 
                       multiple = T,
                       width = '100%'
        )})
    
    
    observeEvent(c(internalValues$gPropsSelected,
                   internalValues$sPropsSelected,
                   internalValues$intensitiesSelected,
                   internalValues$othersSelected,
                   internalValues$rtMin),{
                       
                       updateFT(values)
                       
                       values$featureTables$selectedCols <- unique(unname(c(values$featureTables$tables[[values$featureTables$active]]$core,
                                                                            values$featureTables$tables[[values$featureTables$active]]$comments,
                                                                            internalValues$gPropsSelected,
                                                                            internalValues$sPropsSelected,
                                                                            internalValues$intensitiesSelected,
                                                                            internalValues$othersSelected
                       )))
                   })
    
    observeEvent(c(input$mainSelGroup),
                 {
                     if(!is.null(input$mainSelGroup)){
                         internalValues$selectedGroup <- input$mainSelGroup
                     }
                     internalValues$gPropsSelected <- values$featureTables$tables[[values$featureTables$active]]$gProps[[internalValues$selectedGroup]]
                     internalValues$sPropsSelected <- values$featureTables$tables[[values$featureTables$active]]$sProps[[internalValues$selectedGroup]]
                     internalValues$intensitiesSelected <- values$featureTables$tables[[values$featureTables$active]]$anagroupnames[[internalValues$selectedGroup]]})
    
    observeEvent(c(input$mainSelOthers),
                 {internalValues$othersSelected <- input$mainSelOthers })
    
    return(internalValues)
    
}


#' @describeIn ColumnSelModule UI elements for ColumnSelModule
#' @export 
ColumnSelModuleUI <-  function(id){
    ns <- NS(id)
    
    fluidPage(
        htmlOutput(ns('selnormdata')),
        htmlOutput(ns('mainSelGroup')),
        htmlOutput(ns('mainSelgProps')),
        htmlOutput(ns('mainSelsProps')),
        htmlOutput(ns('mainSelIntensities')),
        htmlOutput(ns('mainSelOthers'))
    )
    
}