## ----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) ) # }) # # })