inst/shiny/PTM_MarkerFinder/server.R

In fgcz/bfabricShiny: A Module for Bridging B-Fabric and R using REST

#
# This is a Shiny web application. 
#
#
#    https://cran.r-project.org/package=protViz
#
# $HeadURL: svn+ssh://cp@fgcz-148.uzh.ch/home/cp/__SUBVERSION_REPOSITORY__/__projects/2016/20160704_pptm_shiny/server.R $
# $Id: server.R 915 2017-04-11 12:36:53Z cp $
# $Date: 2017-04-11 14:36:53 +0200 (Tue, 11 Apr 2017) $


library(bfabricShiny)
library(protViz)
library(PKI)

xy_range_str <- function(e) {
  if(is.null(e)) return(NULL)
  
  paste0("xmin=", round(e$xmin, 1), " xmax=", round(e$xmax, 1), 
         " ymin=", round(e$ymin, 1), " ymax=", round(e$ymax, 1))
  
  return(list(xmin=e$xmin, xmax=e$xmax, ymin=e$ymin, ymax=e$ymax))
}

.ssh_load_RData <- function(host = 'fgcz-r-021.uzh.ch', user = 'cpanse', file = NULL){
  e <- new.env()
  
  cmd <- paste('cat ',  file)
  
  ssh_cmd <- paste("ssh ", user, "@", host, " '", cmd, "'", sep="")
  message(ssh_cmd)
  
  S <- load(pipe(ssh_cmd))
  
  for (x in S){
    assign(x, get(x), e)
  }
  e
}

.load_RData <- function(file = NULL){
  e <- new.env()
  
  S <- load(file)
  
  for (x in S){
    assign(x, get(x), e)
  }
  e
}

shinyServer(function(input, output, session) {
  
  bf <- callModule(bfabric, "bfabric8",  applicationid = c(155))
  
  
  markerIonList <- reactive({list(ADPr = c(428.0367, 348.0704, 250.0935, 136.0618, 524.057827, 542.068392, 560.078957, 559.094941, 584.090190),
                                  Glykan =  c(109.02841, 127.03897, 145.04954, 163.06010, 325.11292),
                                  HexNAc = c(126.05495, 138.05495, 144.06552, 168.06552, 186.07608, 204.08665))})
  
  
  last_click <- reactiveValues(id = NULL)
  #brush.mbb <- reactiveValues(xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL)
  
  output$mZmarkerIons <- renderUI({
    
    markerIons <- sort(c(428.0367, 348.0704, 250.0935, 136.0618, 524.057827,
                           542.068392, 560.078957, 559.094941, 584.090190))
      
      e <- getRDataEnv()
      
      marker <- names(markerIonList())
      
      if (length(ls(e)) > 0){
       # df <- getDataAsDataFrame()
        
        tagList(
          hr(),
          selectInput('mascot_object', 'mascot_object:',  ls(e), multiple = FALSE),
          hr(),
          sliderInput("minMarkerIntensityRatio",
                      "minMarkerIntensityRatio",
                      min = 1,
                      max = 100,
                      value = 10),
          
          sliderInput("minNumberIons",
                      "minNumberIons",
                      min = 1,
                      max = 6,
                      value = 2),
          
          sliderInput("score_cutoff",
                      "mascot score cut-off",
                      min = 0,
                      max = 100,
                      value = 25),
    
          selectInput('mZmarkerIons', 'marker ions:',  markerIons, multiple = TRUE,
                      selected = markerIons),
          
          checkboxGroupInput("plotLines", label = h3("plot lines"), choices = list("yes" = 1), selected = 1),
          checkboxGroupInput("plotLegend", label = h3("plot legend"), choices = list("yes" = 1), selected = 0),
         
          checkboxGroupInput("zoom", label = h3("zoom in"), choices = list("yes" = 1), selected = 0),
          
         sliderInput("xrange", "x-Range:",
                      min = 0, max = 3 * 3600, value = c(0,3*3600)),
          
         sliderInput("yrange", "y-Range:",
                     min =0, max = 2000, value = c(0,3600)),
         
     
          sliderInput("alpha", "alpha blending %", min = 1, max = 100, value = 40),
          sliderInput("alpha_brush", "alpha blending brush%", min = 1, max = 100, value = 20)
    
        )}else{
         text("no data loaded.")
          }
  })
  
  # return an env
  getRDataEnv <- eventReactive(input$load, {
    
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    
    filename <- file.path('/srv/www/htdocs/', input$relativepath)
    filename.cache <- file.path(Sys.getenv("HOME"), 'Downloads', input$relativepath)
  
    if (file.exists(filename)){
      
      progress$set(message = "loading", 
                   detail = paste("file", filename),
                   value = 0.10)
      
      e <- .load_RData(file=filename)
    } else if (file.exists(filename.cache)){
      progress$set(message = "loading via local cache", 
                   detail = paste("file", filename.cache),
                   value = 0.10)
      
      e <- .load_RData(file = filename.cache)
    }else{
      
      progress$set(message = "loading via SSH", 
                   detail = paste("file", filename.cache),
                   value = 0.10)
      
      e <- .ssh_load_RData(file = filename, host = 'fgcz-r-021.uzh.ch')
    }
    
    e.names <- ls(e)
    
    for (idx in 1:length(e.names)){
      nn <- e.names[idx]
      
      progress$inc(0.5 + (idx / (2 * length(e.names))), detail = paste("converting", nn, "into a psmSet object"))
  
      assign (nn, as.psmSet(get(nn, e)), envir = e)
    }
    return (e)
  })
  
 
  
  getData <- eventReactive(input$mascot_object, {
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = paste("converting", input$mascot_object, "into a psmSet object"), value = 0)
    
    # as.psmSet(get(input$mascot_object, getRDataEnv()))
    get(input$mascot_object, getRDataEnv())
  })
  
  
  getDataAsDataFrame <- reactive({
    as.data.frame.psmSet(getData())
  })
  
  processedData0 <- reactive({
    
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "running PTM Marker Finder", value = 0)
    
    
    S <- getData()
    
    mZmarkerIons <- sapply(input$mZmarkerIons, as.numeric)
    
    rv <- findMz(S, 
                 itol_ppm = 10,
                 mZmarkerIons=mZmarkerIons,
                 minMarkerIntensityRatio=input$minMarkerIntensityRatio,
                 minNumberIons=input$minNumberIons
    )
    
  
    rv
  })
  
  processedData <- reactive({
    
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "filter brush", value = 0)
  
    rv <- processedData0()
    
    brush.mbb <- xy_range_str(input$plot_brush)
    
    rv$brush <- FALSE
    
    if (!is.null(brush.mbb)){
      brush <- brush.mbb$xmin < rv$rtinseconds & rv$rtinseconds < brush.mbb$xmax & brush.mbb$ymin < rv$pepmass & rv$pepmass < brush.mbb$ymax
      rv$brush[brush] <- TRUE 
    }
    
    rv
  })
  
  output$findMzTableWide <- DT::renderDataTable(DT::datatable({
    
    S <- processedData();
   
    if (nrow(S) > 0 ){
      SS <- reshape(S[,c(1,4,5,6)], direction='wide', timevar='markerIonMZ', idvar=c('query', 'peptideSequence'))
      return(as.data.frame(SS))
    }else{
      return(as.data.frame(list(output="no data - select a zip file.")))
    }
    
  })
  )
  
  output$findMzTableLong <- DT::renderDataTable(DT::datatable({
   
      S <- processedData();
      
      if (nrow(S) > 0 ){
        return(as.data.frame(S))
      }else{
        return(as.data.frame(list(output="no data - select a zip file.")))
      }
      
    })
  )
  
  output$info <- renderPrint({
    df <- getDataAsDataFrame()
    print(df[last_click$id, ])
  })
  
  
  output$sessionInfo <- renderPrint({
    sessionInfo()
  })
  
  
  output$plot_hoverinfo <- renderText({
    res <- getDataAsDataFrame()
    S <- getData()
    
    xy_str <- function(e) {
      if(is.null(e)) return("NULL\n")
      paste0("x=", round(e$x, 1), " y=", round(e$y, 1), "\n")
    }
    
    xy_range_str <- function(e) {
      if(is.null(e)) return("NULL\n")
      paste0("xmin=", round(e$xmin, 1), " xmax=", round(e$xmax, 1), 
             " ymin=", round(e$ymin, 1), " ymax=", round(e$ymax, 1))
    }
    
    if (!is.null(input$plot_click)){
     rv <- nearPoints(res, input$plot_click, yvar = 'moverz', xvar='RTINSECONDS', maxpoints = 1)
      last_click$id <- as.integer(row.names(rv[1]))
    }
    
    paste0(
      "hover: ", xy_str(input$plot_hover),
      "brush: ", xy_range_str(input$plot_brush),
      "id:", last_click$id
    )
    
  })
  
  output$peakplot_click <- renderPlot({
    S <- getData()
    
    if (!is.null(last_click$id)){
      plot(S[[last_click$id]])  
      abline(v = input$mZmarkerIons ,
             lwd = 4,
             col = rgb(0.1,0.1,0.7, alpha = input$alpha_brush / 100))
    }
  })
  
  output$linkedlcmsmap <- renderPlot({
   
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "making LC MS map ,,,", value = 0)
    
    MSM <- getData()
    MI <- processedData()
    
    if(!is.null(MSM)){
      par(mfrow=c(1,1))
        
      if (1 %in% input$zoom){
       
        lcmsmap(MSM, score.cutoff = input$score_cutoff, 
                charges = as.numeric(input$charges),
                xlim = input$xrange,
                ylim = input$yrange)
      }else{
        lcmsmap(MSM, score.cutoff = input$score_cutoff, charges = as.numeric(input$charges))
      }
      
      MI.filter <- MI[MI$charge %in% as.numeric(input$charges) & MI$score > input$score_cutoff,  ]
      
      points(MI.filter$rtinseconds, MI.filter$pepmass, 
             pch = 22, 
             #col = rgb(0.9,0.1,0.1, alpha = input$alpha/100), 
             cex = 1)
      
      if (!is.null(last_click$id)){
        df <- getDataAsDataFrame()
       # print(df[last_click$id, ])
        points(df$RTINSECONDS[last_click$id], df$moverz[last_click$id], col = rgb(0.1,0.1,0.9, alpha=0.7), cex =2 , pch =16)
      }
      # text(MI.filter$rtinseconds, MI.filter$pepmass, MI.filter$peptideSequence, col = rgb(0.9,0.1,0.1, alpha = 0.3), lwd = 0.5)
  
    }
  })
  
  output$linkedboxplot <- renderPlot({
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "making LC MS map ,,,", value = 0)
    
    MSM <- getData()
    MI <- processedData()
    
   
    if(!is.null(MSM)){
      par(mfrow=c(1,1))
      
      lcmsmap(MSM, score.cutoff = input$score_cutoff, charges = as.numeric(input$charges))
      
      MI.filter <- MI[MI$charge %in% as.numeric(input$charges) & MI$score > input$score_cutoff,  ]
      
      points(MI.filter$rtinseconds, MI.filter$pepmass, 
             #pch = 16, 
             #col = rgb(0.9,0.1,0.1, alpha = input$alpha/100), 
             cex = 2)
      # text(MI.filter$rtinseconds, MI.filter$pepmass, MI.filter$peptideSequence, col = rgb(0.9,0.1,0.1, alpha = 0.3), lwd = 0.5)
      
    }
  })
  
  output$findMzPlot <- renderPlot({
    
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "making PTM MarkerFinder boxplot ,,,", value = 0)
    
    S <- processedData()
    op <- par(mfrow=c(1,1))
    
    
    if (!is.null(S)){
      
      b <- boxplot(markerIonIntensity ~ markerIonMZ,
                   data=S,
                   log = "y",
                   main = input$file,
                   #sub = paste(xy_range_str(input$plot_brush)),
                   xlab = "markerIon m/z",
                   ylab = "log10 based marker ion intensity")
      text(1:length(b$n), b$stats[3,], b$n, col="darkblue", pos=1)
      
      if (1 %in% input$plotLegend){
      legend('topright', legend=sapply(input$mZmarkerIons, as.numeric))
      
      }
      if (1 %in% input$plotLines){
        lines(as.factor(S$markerIonMZ), S$markerIonIntensity, 
              col = rgb(0.1, 0.1, 0.1, alpha = input$alpha / 100),
              lwd = 6)
      }
      if (1 %in% input$plotLegend){
      legend("topleft", c(paste("minNumberIons =", input$minNumberIons),
                          paste("minMarkerIntensityRatio =", input$minMarkerIntensityRatio),
                          paste("Number of queries =",  length(unique(S$query))),
                          paste("Number of psm (score >=", input$score_cutoff, ") =", 
                                sum(S$score >= input$score_cutoff, na.rm=TRUE)),
                          paste("Number of psm (score <", input$score_cutoff, ") =", 
                                sum(S$score < input$score_cutoff, na.rm=TRUE))
      ))}
    }else{
      plot(0,0,
           type='n',
           sub=paste(input$minNumberIons, input$minMarkerIntensityRatio, nrow(S)))
      text(0,0, "no data", cex=3)
    }
    # draw the histogram with the specified number of bins
    #hist(x, breaks = bins, col = 'darkgray', border = 'white')
  })
  

  
  
  output$findMzPlotBrush <- renderPlot({
    
    progress <- shiny::Progress$new()
    on.exit(progress$close())
    progress$set(message = "making PTM MarkerFinder boxplot ,,,", value = 0)
    
    S <- processedData()
    
    op <- par(mfrow=c(1,1))
    
    if (!is.null(S)){
      b <- boxplot(markerIonIntensity ~ markerIonMZ,
                   data=S,
                   log = "y",
                   main = input$file,
                   #sub = paste(xy_range_str(input$plot_brush)),
                   xlab = "markerIon m/z",
                   ylab = "log10 based marker ion intensity")
      
      text(1:length(b$n), b$stats[3,], b$n, col="darkblue", pos=1)
      
      if (1 %in% input$plotLegend){
      legend('topright', legend=sapply(input$mZmarkerIons, as.numeric))
      }
      if (1 %in% input$plotLines){
        
        lines(as.factor(S$markerIonMZ[!S$brush]), S$markerIonIntensity[!S$brush], 
                col=rgb(0.1,0.1,0.1, alpha = input$alpha / 100),
                lwd=3)
          
        lines(as.factor(S$markerIonMZ[S$brush]), S$markerIonIntensity[S$brush], 
                col=rgb(0.95,0.1,0.1, alpha=input$alpha_brush / 100),
                lwd=6)
      }
      
      if (1 %in% input$plotLegend){
        legend("topleft", c(paste("minNumberIons =", input$minNumberIons),
                            paste("minMarkerIntensityRatio =", input$minMarkerIntensityRatio),
                            paste("Number of queries =",  length(unique(S$query))),
                            paste("Number of psm (score >=", input$score_cutoff, ") =", 
                                  sum(S$score >= input$score_cutoff, na.rm=TRUE)),
                            paste("Number of psm (score <", input$score_cutoff, ") =", 
                                  sum(S$score < input$score_cutoff, na.rm=TRUE))
        ))}
    }else{
      plot(0,0,
           type='n',
           sub=paste(input$minNumberIons, input$minMarkerIntensityRatio, nrow(S)))
      text(0,0, "no data", cex=3)
    }
    # draw the histogram with the specified number of bins
    #hist(x, breaks = bins, col = 'darkgray', border = 'white')
  })
  
  
  
  output$downloadData <- downloadHandler(
    filename = function() { paste(unlist(strsplit(input$mascot_object, 
                                                  split="[.]"))[1], "csv", sep=".")  },
    content = function(file) {
      write.csv(processedData(), file, row.names = FALSE)
    }
  )
  
  output$downloadDataWide <- downloadHandler(
    filename = function() { paste(unlist(strsplit(input$mascot_object, 
                                                  split="[.]"))[1], "wide", "csv", sep=".")  },
    content = function(file) {
      S <- processedData()
      SS <- reshape(S[,c(1,4,5,6)], direction='wide', timevar='markerIonMZ', idvar=c('query', 'peptideSequence'))
      write.csv(SS, file, row.names = FALSE)
    }
    
  )
  output$downloadMgf <- downloadHandler(
    filename = function() { paste(unlist(strsplit(input$mascot_object, 
                                                  split="[.]"))[1], "mgf", sep=".")  },
    content = function(file) {
      res <- list(summary = processedData(),
                  PsmSet=getData())
      
      protViz:::.PTM_MarkerFinder_writeMGF_Header(file)
      dump <- lapply(unique(res$summary$query), 
                     function(idx){
                       pattern <- res$summary[res$summary$query==idx, c(5, 4)]
                       psm <- res$PsmSet[[idx]]
                       psm$title <- psm$fileName
                       psm$rtinseconds <- psm$rt
                       psm$scans <- psm$id
                       protViz:::.PTM_MarkerFinder_writeMGF(psm, file, pattern = pattern)
                     })
      #write.csv(processData(input), file, row.names = FALSE)
    }
  )
  output$download <- renderUI({
    S <- processedData()
    if (!is.null(S)){
      tagList(
        downloadButton('downloadData', 'Download'),
        downloadButton('downloadDataWide', 'Download (wide)'),
        downloadButton('downloadMgf', 'Generate MGF(under construction!)'))}
  })
})