## ----, eval=FALSE--------------------------------------------------------
## library(shiny)
## shinyUI(pageWithSidebar(
##   # Application title
##   headerPanel("Simple Genome Browser"),
##   # Sidebar with a slider inputs and selection boxes
##   sidebarPanel(
##     sliderInput("windowsize",
##                 "Windowsize:",
##                 min = 10,
##                 max = 200,
##                 value = 50,
##                 step = 5),
##     uiOutput("chromSelect"),
##     uiOutput("genomicPositionSelect")
##   ),
##   # Show a plot of the region
##   mainPanel(
##     plotOutput("mismatchPlot", height=800)
##   )
## ))


## ----, eval=FALSE--------------------------------------------------------
## library(shiny)
## library(h5vc)
## library(rhdf5)
## tallyFile <- "yeast.hfs5"
## study <- "/yeast"
## h5ls( tallyFile )
## chromosomes  <- h5ls( tallyFile )
## chromlengths <- as.numeric(subset( chromosomes, otype == "H5I_DATASET" & name == "Reference" )$dim)
## chromosomes  <- subset( chromosomes, otype == "H5I_GROUP" & name != "yeast" )$name
## names(chromlengths) = chromosomes
## 
## # Define server logic required to generate and plot a random distribution
## shinyServer(function(input, output) {
## 
##   output$chromSelect <- renderUI({
##     selectInput( "chrom", "Chromosome", choices = c("I","II","III","IV","V","VI","VII","VIII","IX","X","XI","XII","XIII","XIV","XV","XVI", "Mito"))
##   })
## 
##   output$genomicPositionSelect <- renderUI({
##     sliderInput( "gpos", "Genomic Position:", min = 10, max = chromlengths[input$chrom] - 10, value = 200 )
##   })
## 
##   group <- reactive({ paste( study, input$chrom, sep="/" ) })
## 
##   sampleData <- reactive({ sd = getSampleData( tallyFile, group() ); sd$Sample = c("YB210","s288c"); sd })
## 
##   pos <- reactive({
##     min( max( input$windowsize + 1, input$gpos ), chromlengths[input$chrom] - input$windowsize - 1 )
##   })
## 
##   data <- reactive({
##     h5dapply(
##       tallyFile,
##       group(),
##       blocksize = input$windowsize*3,
##       names = c("Coverages","Counts","Deletions"),
##       range = c( max( pos() - input$windowsize, 0 ), min( pos() + input$windowsize, chromlengths[input$chrom] )  )
##     )[[1]]
## 
##   })
## 
##   output$mismatchPlot <- renderPlot({
##     p = mismatchPlot(
##       data(),
##       sampleData(),
##       samples = c("s288c","YB210"),
##       input$windowsize,
##       pos()
##       )
##     print(p)
##   })
## })


## ----, eval=FALSE--------------------------------------------------------
## library(rhdf5)
## library(h5vc)
## setwd("~/ShinyApps/Yeast")
## tallyFile <- "yeast.hfs5"
## study <- "/yeast"
## h5ls( tallyFile )
## chromosomes <- h5ls( tallyFile )
## chromosomes <- subset( chromosomes, otype == "H5I_GROUP" & name != "yeast" )$name
## variantCalls <- list()
## for( chrom in chromosomes ){
##   group <- paste( study, chrom, sep = "/" )
##   sdat <- getSampleData( tallyFile, group )
##   sdat$Group <- "yeast"
##   variantCalls[[chrom]] <- h5dapply(
##     filename = tallyFile,
##     group = group,
##     blocksize = 100000,
##     FUN = callVariantsPairedFancy,
##     sampledata = sdat,
##     cl = vcConfParams( returnDataPoints = TRUE, minStrandAltSupport = 4 ),
##     names = c( "Counts", "Coverages", "Reference" ),
##     verbose = TRUE
##   )
## }
## for( chrom in chromosomes ){
##   variantCalls[[chrom]] <- do.call( rbind, variantCalls[[chrom]] )
## }
## variantCalls <- do.call( rbind, variantCalls )
## rownames(variantCalls) = NULL
## variantCalls$Support = variantCalls$caseCountFwd + variantCalls$caseCountRev
## variantCalls$Coverage = variantCalls$caseCoverageFwd + variantCalls$caseCoverageRev
## variantCalls$AF = variantCalls$Support / variantCalls$Coverage
## save( variantCalls, file = "yeast.variants.RDa" )


## ----, eval=FALSE--------------------------------------------------------
## library(shiny)
## shinyUI(pageWithSidebar(
## 
##   # Application title
##   headerPanel("Simple Variant Browser - Yeast Strains Example"),
## 
##   # Sidebar with a slider inputs and selection boxes
##   sidebarPanel(
##     sliderInput("windowsize",
##                 "Windowsize:",
##                 min = 10,
##                 max = 200,
##                 value = 50,
##                 step = 5),
##     uiOutput("chromSelect"),
##     sliderInput("af",
##                 "Allele Frequency:",
##                 min = 0,
##                 max = 1,
##                 value = c(0.1,1.0),
##                 step = 0.01),
##     sliderInput( "minSupport",
##                  "Minimum Support",
##                  min = 2,
##                  max = 200,
##                  value = 2),
##     sliderInput( "minCoverage",
##                  "Minimum Coverage",
##                  min = 10,
##                  max = 500,
##                  value = 50,
##                  step = 5),
##     uiOutput("variantSelect"),
##     textOutput("diag")
##   ),
## 
##   # Show a plot of the region
##   mainPanel(
##     tabsetPanel(
##       tabPanel( title = "Region Mismatch Plot", plotOutput("mismatchPlot", height=800) ),
##       tabPanel( title = "Variant Table", tableOutput("variantTable") ),
##       tabPanel( title = "Variant Summary Plots", plotOutput("afHist") )
##     )
##   )
## ))


## ----, eval=FALSE--------------------------------------------------------
## library(shiny)
## library(h5vc)
## library(rhdf5)
## library(ggplot2)
## library(grid)
## 
## tallyFile <- "yeast.hfs5"
## study <- "/yeast"
## h5ls( tallyFile )
## chromosomes  = h5ls( tallyFile )
## chromlengths = as.numeric(subset( chromosomes, otype == "H5I_DATASET" & name == "Reference" )$dim)
## chromosomes  = subset( chromosomes, otype == "H5I_GROUP" & name != "yeast" )$name
## names(chromlengths) = chromosomes
## 
## load(file="yeast.variants.RDa")
## variantCalls$start <- variantCalls$start + 1 #fixing difference in counting 0-based vs. 1-based
## variantCalls$end <- variantCalls$end + 1
## # Define server logic required to generate and plot a random distribution
## shinyServer(function(input, output) {
## 
##   output$chromSelect <- renderUI({
##     selectInput( "chrom", "Chromosome", choices = c("I","II","III","IV","V","VI","VII","VIII","IX","X","XI","XII","XIII","XIV","XV","XVI", "Mito"))
##   })
## 
##   group <- reactive({ paste( study, input$chrom, sep="/" ) })
## 
##   sampleData <- reactive({ sd = getSampleData( tallyFile, group() ); sd$Sample = c("YB210","s288c"); sd })
## 
##   variants <- reactive({
##     subset( variantCalls, seqnames == input$chrom & AF >= input$af[1] & AF <= input$af[2] & Support >= input$minSupport & Coverage >= input$minCoverage )
##   })
## 
##   output$variantSelect <- renderUI({
##     tmp = seq(nrow(variants()))
##     names(tmp) =  paste( variants()$start, " - ", variants()$refAllele, "/", variants()$altAllele, sep="" )
##     selectInput( "var", "Variant:", choices = tmp )
##   })
## 
##   pos <- reactive({
##     variants()$start[as.numeric(input$var)]
##   })
## 
##   data <- reactive({
##     if( nrow(variants()) > 0 ){
##       h5dapply(
##         filename = tallyFile,
##         group = group(),
##         blocksize = input$windowsize*3,
##         names = c("Coverages","Counts","Deletions"),
##         range = c( max( pos() - input$windowsize, 0 ), min( pos() + input$windowsize, chromlengths[input$chrom] )  )
##       )[[1]]
##     }else{
##       NULL
##     }
##   })
## 
##   output$mismatchPlot <- renderPlot({
##     if( nrow(variants()) > 0 ){
##       p = mismatchPlot(
##         data(),
##         sampleData(),
##         samples = c("s288c","YB210"),
##         input$windowsize,
##         pos()
##       )
##       print(p)
##     }
##   })
## 
##   output$variantTable <- renderTable({
##     variants()[,c("seqnames", "start", "refAllele", "altAllele", "AF", "Support", "Coverage")]
##   })
## 
##   output$afHist = renderPlot({
##     hist( variants()$AF, breaks = seq(0,1,0.01) )
##   })
## 
## })