R/module_mirrorPlots.R

In chasemc/IDBac_App: MALDI-TOF MS Protien and Small Molecule Analysis

#' mirrorPlotsSettings_UI
#'
#' @param id namespace
#'
#' @return NA
#' 
#'
mirrorPlotsSettings_UI <- function(id){
  ns <- NS(id)
  uiOutput(ns("mirrorSpectraSelector"))
}

#' mirrorPlotDownload_UI
#'
#' @param id namespace
#'
#' @return NA
#' 
#'
mirrorPlotDownload_UI <- function(id){
  ns <- NS(id)
  tagList(
    downloadButton(ns("downloadInverse"), 
                   label = "Download SVG"),
    uiOutput(ns("normSpecUi"))
    
  )
  
}  

#' mirrorPlots_UI
#'
#' @param id  namespace
#'
#' @return NA
#' 
#'
mirrorPlots_UI <- function(id){
  ns <- NS(id)
  fluidRow(
    shinycssloaders::withSpinner(
      plotly::plotlyOutput(ns("inversePeakComparisonPlot")
      )
      
    ))
  
}

#' Title
#'
#' @param input shiny
#' @param output shiny
#' @param session shiny
#' @param workingDB reactive containing SQLite DB pool
#' @param proteinOrSmall  '>' for protein '<' for small mol
#'
#' @return NA
#' 
#'
mirrorPlots_Server <- function(input,
                               output,
                               session,
                               workingDB,
                               proteinOrSmall){
  
  
  
  output$normSpecUi <- renderUI({
    
    radioButtons(session$ns("normSpec"),
                 label = ("Normalize Spectra?"),
                 choices = list("Raw Spectra" = 1L, 
                                "Normalized" = 2L), 
                 selected = 1L)
    
  })
  
  
  
  inverseComparisonNames <- reactive({
    conn <- pool::poolCheckout(workingDB$pool())
    
    a <- DBI::dbGetQuery(conn, glue::glue("SELECT DISTINCT strain_id
                                            FROM spectra
                                            WHERE max_mass {proteinOrSmall} 6000"))
    pool::poolReturn(conn)
    
    a[ , 1]
    
  })
  
  
  
  output$mirrorSpectraSelector <- renderUI({
    
    tagList(
      tags$div(id = 'proteinMirror',
               class = 'mirror_select',
               column(width = 5, offset = 1,
                      selectizeInput(session$ns("Spectra1"), 
                                     label = strong("Spectrum 1 (positive y-axis)"),
                                     options = list(maxOptions = 10000),
                                     choices = c("Choose one" = "", inverseComparisonNames()))
               ),
               column(width = 6,
                      selectizeInput(session$ns("Spectra2"),
                                     label = strong("Spectrum 2 (negative y-axis)"),
                                     options = list(maxOptions = 10000),
                                     choices = c("Choose one" = "", inverseComparisonNames()))
               )
      )
    )
    
  })
  
  
  
  
  
  dataForInversePeakComparisonPlot <- reactive({
    
    req(input$Spectra1 %in% idbac_available_samples(workingDB$pool(), type= "protein"))
    req(input$Spectra2 %in% idbac_available_samples(workingDB$pool(), type= "protein"))
    
    if (input$normSpec == 1L) {
      normalizeSpectra <- FALSE
    } else if (input$normSpec == 2L) {
      normalizeSpectra <- TRUE
    }
    
    
    assembleMirrorPlots(sampleID1 = input$Spectra1,
                        sampleID2 = input$Spectra2,
                        minFrequency = input$percentPresence,
                        lowerMassCutoff = input$lowerMass,
                        upperMassCutoff = input$upperMass,
                        minSNR = input$SNR,
                        tolerance = 0.002,
                        pool1 = workingDB$pool(),
                        pool2 = workingDB$pool(),
                        normalizeSpectra = normalizeSpectra)
  })
  
  # Used in the the inverse-peak plot for zooming ---------------------------
  
  ranges2 <- reactiveValues(x = NULL, y = NULL)
  
  
  
  
  # Output for the non-zoomed mirror plot
  output$inversePeakComparisonPlot <- plotly::renderPlotly({
    
    mirrorPlot(mirrorPlotEnv = dataForInversePeakComparisonPlot())
    
    
  })
  
  
  # Output the zoomed mirror plot -------------------------------------------
  
  
  # Download svg of zoomed mirror plot --------------------------------------
  
  output$downloadInverse <- downloadHandler(
    filename = function(){paste0("top-",input$Spectra1,"_","bottom-",input$Spectra2,"-Zoom.svg")
    },
    content = function(file1){
      
      svglite::svglite(file1, width = 10, height = 8, bg = "white",
                       pointsize = 12, standalone = TRUE)
      
      baserMirrorPlot(mirrorPlotEnv = dataForInversePeakComparisonPlot())
      
      grDevices::dev.off()
      
      if (file.exists(paste0(file1, ".svg")))
        #TODO why
        file.rename(paste0(file1, ".svg"), file1)
      
    })
  
  
  
  
  
}