Author: Martin Morgan (mtmorgan@fredhutch.org)
Date: 7 September, 2015
Back to Workshop Outline

The material in this document requires R version 3.2 and Bioconductor version 3.1

stopifnot(
    getRversion() >= '3.2' && getRversion() < '3.3',
    BiocInstaller::biocVersion() >= "3.1"
)

Interactive visualization – shiny

Writing a shiny app

• 'User interface' describing what the user sees
• 'Server' implementing the logic that transforms user selections to outputs
• Very interesting 'reactive' programming model; sort of like an Excel spread sheet, where changing a cell causes a formula in another cell to update.

A simple directory with user interface (ui.R) and server (server.R) R scripts

• User interface, file ui.R

  library(shiny)
  library(RNAseqData.HNRNPC.bam.chr14)
  library(Homo.sapiens)
  
  ## Get all SYMBOLs on chr14
  symbols <- keys(Homo.sapiens, keytype="SYMBOL")
  map <- select(Homo.sapiens, symbols, "TXCHROM", "SYMBOL")
  symchoices <- sort(unique(map$SYMBOL[map$TXCHROM %in% "chr14"]))
  
  ## Possible BAM files
  bamchoices <- basename(RNAseqData.HNRNPC.bam.chr14_BAMFILES)
  
  ## Define the user interface
  shinyUI(fluidPage(
  
      ## Application title
      titlePanel("BAMSpector: Reads Supporting Gene Models"),
  
      sidebarLayout(
          sidebarPanel(
              ## input gene symbol (fancy: select from available)
              selectInput("symbol", "Gene Symbol", symchoices),
  
              ## input path to BAM file
              selectInput("bam", "BAM File", bamchoices, multiple=TRUE)),
  
          ## Show a plot of the generated distribution
          mainPanel(plotOutput("tracksPlot")))
      ))
  

• Server, file server.R

  ## load required libraries
  library(shiny)
  library(RNAseqData.HNRNPC.bam.chr14)
  library(Homo.sapiens)
  library(Gviz)
  
  ## where are the BAM files?
  dirname <- unique(dirname(RNAseqData.HNRNPC.bam.chr14_BAMFILES))
  
  ## What are the ranges of each gene?
  ranges <- genes(Homo.sapiens, columns="SYMBOL")
  ranges$SYMBOL <- unlist(ranges$SYMBOL)
  
  ## Create a representation of each gene region
  genes <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg19.knownGene,
                           chromosome="chr14")
  
  shinyServer(function(input, output) {
  
      output$tracksPlot <- renderPlot({
          if (length(input$bam) > 0) {
              ## coverage on each BAM file
              bam <- file.path(dirname, input$bam)
              coverage <- Map(DataTrack,
                  range = bam, name = bam,
                  MoreArgs=list(type = 'histogram',
                      window = -1, genome = 'hg19',
                      chromosome = 'chr14'))
          } else {
              coverage <- list()
          }
  
          ## Select the correct range
          range <- ranges[match(input$symbol, ranges$SYMBOL)]
  
          ## plot the GeneRegionTrack and coverage
          plotTracks(c(list(genes), coverage),
                     from = start(range), to=end(range),
                     chr='chr14', windowSize = 30)
      })
  })
  

• Application

  shiny::runApp()