R/module_convertBruker.R

In chasemc/ghosts: Protein and small molecule analysis of bacteria by MALDI-TOF MS

#' oneMaldiPlate
#'
#' @param id NA
#'
#' @return NA
#' @export
#'

convertOneBruker_UI <- function(id){
  ns <- NS(id)
  tagList( 
    h3("Starting with a single MALDI plate of Bruker data", align = "center"),
    p(strong("1: Enter a name for this new experiment")),
    p("This will become a filename, non-valid characters will be removed."),
    p("Hint: Intead of a space, use \"_\"."),
    textInput(ns("newExperimentName"),
              label = "",
              width = "50%",
              placeholder = "Enter Experiment Name Here"),
    verbatimTextOutput(ns("newExperimentNameText"),
                       placeholder = TRUE),
    tags$hr(size = 20),
    p(strong("2: Click to select your folder that contains data from a single MALDI plate."), align = "center"),
    actionButton(ns("rawFileDirectory"),
                 label = "Raw Data Folder"),
    verbatimTextOutput(ns("rawFileDirectoryText"),
                       placeholder = TRUE),
    tags$hr(size = 20),
    p(strong("3:", "Fill in the Sample-ID spreadsheet.")),
    
    actionButton(ns("showSampleMap"), "Click to Open Spreadsheet"),
    tags$hr(size = 20),
    p(strong("You must label all spots that contain data."), br(),
      strong("defb found data for the following spots that aren't labelled in the spreadsheet:")
    ),
    shiny::verbatimTextOutput(ns("missingSampleNames"), placeholder = TRUE),
    p(strong("4:","Click \"Process Data\" to begin spectra conversion.")),
    actionButton(ns("convertSingleBruker"),
                 label = "Process Data"),
    tags$hr(size = 20)
  )
  
}





#' convertOneBruker_Server
#'
#' @param input NS
#' @param output NS
#' @param session NS
#' @param tempMZDir tempMZDir 
#' @param sqlDirectory sqlDirectory
#' @param availableExperiments availableExperiments
#'
#' @return NA
#'
convertOneBruker_Server <- function(input,
                                    output,
                                    session,
                                    tempMZDir,
                                    sqlDirectory,
                                    availableExperiments){
  
  
  
  # Reactive variable returning the user-chosen location of the raw MALDI files as string
  #----
  rawFilesLocation <- reactive({
    if (input$rawFileDirectory > 0) {
      loc <- ghosts::choose_dir()
      
      if (!is.na(loc)) {
        return(loc)
      }
    }
  })
  
  
  sanitizedNewExperimentName <- reactive({
    
    ghosts::path_sanitize(input$newExperimentName)
    
  })
  
  
  output$newExperimentNameText <- renderText({
    
    sanitized <- sanitizedNewExperimentName()
    
    if (sanitized == "") {
      return("The filename-friendly version of your entry will appear here.")
    } else {
      return(sanitized)
    }
  })
  
  
  # Creates text showing the user which directory they chose for raw files
  #----
  output$rawFileDirectoryText <- renderText({
    
    if (is.null(rawFilesLocation())) {
      
      return("No Folder Selected")
      
    } else {
      
      folders <- NULL
      # Get the folders contained within the chosen folder.
      foldersInFolder <- list.dirs(rawFilesLocation(),
                                   recursive = FALSE,
                                   full.names = FALSE) 
      for (i in 1:length(foldersInFolder)) {
        # Creates user feedback about which raw data folders were chosen.  Individual folders displayed on a new line "\n"
        folders <- paste0(folders, 
                          "\n",
                          foldersInFolder[[i]])
      }
      return(folders)
    }
  })
  
  
  # Reactive variable returning the user-chosen location of the raw MALDI files as string
  #----
  multipleMaldiRawFileLocation <- reactive({
    if (input$multipleMaldiRawFileDirectory > 0) {
      ghosts::choose_dir()
    }
  })
  
  
  # Creates text showing the user which directory they chose for raw files
  #----
  output$multipleMaldiRawFileDirectory <- renderText({
    if (is.null(multipleMaldiRawFileLocation())) {
      return("No Folder Selected")
    } else {
      folders <- NULL
      # Get the folders contained within the chosen folder.
      foldersInFolder <- list.dirs(multipleMaldiRawFileLocation(),
                                   recursive = FALSE, 
                                   full.names = FALSE) 
      for (i in 1:length(foldersInFolder)) {
        # Creates user feedback about which raw data folders were chosen. 
        # Individual folders displayed on a new line "\n"
        folders <- paste0(folders, "\n", foldersInFolder[[i]]) 
      }
      
      return(folders)
    }
  })
  
  
  # list of acqus info
  acquisitonInformation <- reactive({
    
    ghosts::readBrukerAcqus(rawFilesLocation())
    
  })
  
  
  
  # Sample Map --------------------------------------------------------------
  
  anyMissing <- reactive({
    
    req(rawFilesLocation())
    req(sampleMapReactive$rt)
    
  
    spots <- unlist(lapply(acquisitonInformation(), function(x) x$spot))
    
    ghosts::findMissingSampleMapIds(spots = spots, 
                                      sampleMap = sampleMapReactive$rt)
  })
  
  
  output$missingSampleNames <- shiny::renderText({
    
    if (length(anyMissing()$missing) == 0) {
      paste0("No missing IDs")
    } else {
      paste0(paste0(anyMissing()$missing, collapse = " \n ", sep = ","))
    }
  })
  
  sampleMapReactive <- reactiveValues(rt = ghosts::nulledMap384Well())
  
  observeEvent(input$showSampleMap, 
               ignoreInit = TRUE, {  
                 ns <- session$ns
                 showModal(modalDialog(footer = actionButton(ns("saveSampleMap"), "Save/Close"),{
                   tagList(
                     HTML("This spreadsheet represents a MALDI plate and will work with plate sizes of 384-spots or less. <br>
                          Enter sample names as they were arranged on your MALDI plate. <br>
                          You can also copy/paste from Excel."),
                     rhandsontable::rHandsontableOutput(ns("plateDefault"))
                     
                   )
                 }))
                 
                 
                 
               })
  
  
  output$plateDefault <- rhandsontable::renderRHandsontable({
    
    ghosts::sampleMapViewer(sampleMapReactive$rt)
    
  })
  
  
  observeEvent(input$saveSampleMap, 
               ignoreInit = TRUE, {
                 sampleMapSaver(sampleData = input$plateDefault,
                                sampleMapReactive = sampleMapReactive)
                 
                 shiny::removeModal()
               })
  
  
  
  
  
  
  
  
  success <- reactiveValues(val = FALSE)
  
  # Call the Spectra processing function when the spectra processing button is pressed
  #----
  observeEvent(input$convertSingleBruker,
               ignoreInit = TRUE,  {
                 
                 req(length(anyMissing()$missing) == 0)
                 req(!is.null(sanitizedNewExperimentName()))
                 req(sanitizedNewExperimentName() != "")
                 validate(need(any(!is.na(sampleMapReactive$rt)), 
                               "No samples entered into sample map, please try entering them again"))
                 
                 
                 rawFilesLocation2 <<- rawFilesLocation()
                 inputIds <<- sampleMapReactive$rt
                 
                 
                 
                 # get target positions in order of acqus list
                 spots <- unlist(lapply(acquisitonInformation(), function(x){
                   x$spot
                 }))
                 
                 
            
                 wq <<- acquisitonInformation()
                 wq2<<-anyMissing()$matching
                 
                 # should be the same because both come from acquisitonInformation()
                 validate(need(identical(names(anyMissing()$matching), 
                                         spots),
                               list("Something happend when associating Bruker acqu spots", "\n",
                                    "names:", names(anyMissing()$matching), "\n",
                                    "spots:", spots)
                 ))
                
                  validate(need(identical(length(anyMissing()$matching),
                                         length(acquisitonInformation())),
                               list("Something happend when associating Bruker acqu spots", "\n",
                                    "length(anyMissing()$matching):", length(anyMissing()$matching), "\n",
                                    "length(acquisitonInformation()):", length(acquisitonInformation())
                 )))
                 
                  
                  acquisitionInfo <- split(acquisitonInformation(), anyMissing()$matching) 
                  wwq<<-acquisitionInfo
                
                  files <- lapply(acquisitionInfo, function(x){
                    lapply(x, function(y) y$file)
                  })
                  
                  
                  
                  ghosts::brukerToMzml_popup()
                  
                  
                  
                  forProcessing <- ghosts::proteoWizConvert(msconvertPath = "",
                                                              samplePathList = files,
                                                              convertWhere = tempMZDir)
                  
                  ghosts::popup3()
                  
                  ghosts::processMZML(mzFilePaths = forProcessing$mzFile,
                                        sampleIds = forProcessing$sampleID,
                                        sqlDirectory = sqlDirectory$sqlDirectory,
                                        newExperimentName = sanitizedNewExperimentName(),
                                        acquisitionInfo = acquisitionInfo )
                  
                  # Update available experiments
                  availableExperiments$db <- tools::file_path_sans_ext(list.files(sqlDirectory$sqlDirectory,
                                                                                  pattern = ".sqlite",
                                                                                  full.names = FALSE))
                  ghosts::popup4()
                  
               })
  
}








#' Editable Sample Map 
#'
#' @param df reactiveValues data frame input ghosts::nulledMap384Well()
#'
#' @return rhandsontable
#' @export
#'
sampleMapViewer <- function(df){
  rhandsontable::rhandsontable(df,
                               useTypes = FALSE,
                               contextMenu = TRUE,
                               maxRows = 16,
                               maxRows = 24) %>%
    rhandsontable::hot_context_menu(allowRowEdit = FALSE,
                                    allowColEdit = FALSE) %>%
    rhandsontable::hot_cols(colWidths = 100) %>%
    rhandsontable::hot_rows(rowHeights = 25) 
}



#' Update sample map reactive value
#'
#' @param sampleData sample map rhandsontable
#' @param sampleMapReactive sample map reactive value to save to
#'
#' @return none, side effect
#' @export
#'
sampleMapSaver <- function(sampleData,
                           sampleMapReactive){
  temp <- rhandsontable::hot_to_r(sampleData)
  sampleMapReactive$rt <- as.data.frame(temp, 
                                        stringsAsFactors = FALSE)
  
}