## ----style, echo = FALSE, results = 'asis'--------------------------------------------------------
BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE--------------------------------------------
suppressPackageStartupMessages({
    library(shiny)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(Homo.sapiens)
    library(Gviz)
})

## ----shiny-ui, eval=FALSE-------------------------------------------------------------------------
#  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")))
#      ))

## ----shiny-server, eval=FALSE---------------------------------------------------------------------
#  ## 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)
#      })
#  })

## ----shiny-launch, eval=FALSE---------------------------------------------------------------------
#  shiny::runApp()