library(shiny)
library(igvShiny)
library(GenomicAlignments)
#----------------------------------------------------------------------------------------------------
f <- system.file(package="igvShiny", "extdata", "gwas.RData")
stopifnot(file.exists(f))
tbl.gwas <- get(load(f))
print(dim(tbl.gwas))
printf <- function(...) print(noquote(sprintf(...)))
ns.sep <- "."
#----------------------------------------------------------------------------------------------------
tbl.bed <- data.frame(chr=c("1","1", "1"),
start=c(7432951, 7437000, 7438000),
end= c(7436000, 7437500, 7440000),
value=c(-2.239, 3.0, 0.5),
sampleID=c("sample1", "sample2", "sample3"),
stringsAsFactors=FALSE)
#----------------------------------------------------------------------------------------------------
igv_ui = function(id){
ns <- NS(id)
printf("namespace: '%s'", ns("foo"))
shinyUI(fluidPage(
sidebarLayout(
sidebarPanel(
actionButton(ns("searchButton"), "Search"),
textInput(ns("roi"), label=""),
h5("One simple data.frame, three igv formats:"),
actionButton(ns("addBedTrackButton"), "Add as Bed"),
actionButton(ns("addBedGraphTrackButton"), "Add as BedGraph"),
actionButton(ns("addSegTrackButton"), "Add as SEG"),
br(),
actionButton(ns("addGwasTrackButton"), "Add GWAS Track"),
actionButton(ns("addBamViaHttpButton"), "BAM from URL"),
actionButton(ns("addBamLocalFileButton"), "BAM local data"),
actionButton(ns("addCramViaHttpButton"), "CRAM from URL"),
actionButton(ns("removeUserTracksButton"), "Remove User Tracks"),
actionButton(ns("getChromLocButton"), "Get Region"),
actionButton(ns("clearChromLocButton"), "Clear Region"),
div(style="background-color: white; width: 200px; height:30px; padding-left: 5px;
margin-top: 10px; border: 1px solid blue;",
htmlOutput(ns("chromLocDisplay"))),
hr(),
width=2
),
mainPanel(
igvShinyOutput(ns('igvShiny_0')),
# igvShinyOutput('igvShiny_1'),
width=10
)
) # sidebarLayout
))
}
#----------------------------------------------------------------------------------------------------
igv_server <- function(input, output, session) {
ns <- session$ns
observeEvent(input$searchButton, {
printf("--- search")
searchString = isolate(input$roi)
if(nchar(searchString) > 0)
showGenomicRegion(session, id="igvShiny_0", searchString)
})
observeEvent(input$addBedTrackButton, {
showGenomicRegion(session, id=ns("igvShiny_0"), "chr1:7,426,231-7,453,241")
loadBedTrack(session, id=ns("igvShiny_0"), trackName="bed", tbl=tbl.bed, color="green");
})
observeEvent(input$addBedGraphTrackButton, {
showGenomicRegion(session, id=ns("igvShiny_0"), "chr1:7,426,231-7,453,241")
loadBedGraphTrack(session, id=ns("igvShiny_0"), trackName="wig", tbl=tbl.bed, color="blue", autoscale=TRUE)
})
observeEvent(input$addSegTrackButton, {
showGenomicRegion(session, id=ns("igvShiny_0"), "chr1:7,426,231-7,453,241")
loadSegTrack(session, id=ns("igvShiny_0"), trackName="seg", tbl=tbl.bed)
})
observeEvent(input$addGwasTrackButton, {
printf("---- addGWASTrack")
printf("current working directory: %s", getwd())
showGenomicRegion(session, id=ns("igvShiny_0"), "chr19:45,248,108-45,564,645")
loadGwasTrack(session, id=ns("igvShiny_0"), trackName="gwas", tbl=tbl.gwas, deleteTracksOfSameName=FALSE)
})
observeEvent(input$addBamViaHttpButton, {
printf("---- addBamViaHttpTrack")
showGenomicRegion(session, id=ns("igvShiny_0"), "chr5:88,733,959-88,761,606")
base.url <- "https://1000genomes.s3.amazonaws.com/phase3/data/HG02450/alignment"
url <- sprintf("%s/%s", base.url, "HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam")
indexURL <- sprintf("%s/%s", base.url, "HG02450.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam.bai")
loadBamTrackFromURL(session, id=ns("igvShiny_0"),trackName="1kg.bam", bamURL=url, indexURL=indexURL)
})
observeEvent(input$addBamLocalFileButton, {
printf("---- addBamLocalFileButton")
showGenomicRegion(session, id=ns("igvShiny_0"), "chr21:10,397,614-10,423,341")
bamFile <- system.file(package="igvShiny", "extdata", "tumor.bam")
x <- readGAlignments(bamFile)
loadBamTrackFromLocalData(session, id=ns("igvShiny_0"), trackName="tumor.bam", data=x)
})
observeEvent(input$addCramViaHttpButton, {
printf("---- addCramViaHttpTrack")
showGenomicRegion(session, id=ns("igvShiny_0"), "chr5:88,733,959-88,761,606")
base.url <- "https://s3.amazonaws.com/1000genomes"
url <- sprintf("%s/%s", base.url, "1000G_2504_high_coverage/additional_698_related/data/ERR3989250/HG04160.final.cram")
indexURL <- sprintf("%s.%s", url, "crai")
loadCramTrackFromURL(session, id=ns("igvShiny_0"),trackName="CRAM", cramURL=url, indexURL=indexURL)
})
observeEvent(input$removeUserTracksButton, {
printf("---- removeUserTracks")
removeUserAddedTracks(session, id=ns("igvShiny_0"))
})
observeEvent(input$trackClick, {
printf("--- trackclick event")
x <- input$trackClick
print(x)
})
observeEvent(input$getChromLocButton, {
# printf("--- getChromLoc event")
# sends message to igv.js in browser; currentGenomicRegion.<id> event sent back
# see below for how that can be captured and displayed
getGenomicRegion(session, id=ns("igvShiny_0"))
print(sprintf("getChromLocButton, currentGenomicRegion.%s", ns("igvShiny_0")))
})
observeEvent(input$clearChromLocButton, {
printf("clearing chromLocDisplay after clearChromLocButton click")
printf("---- names(input)")
print(names(input))
output$chromLocDisplay <- renderText({" "})
})
observeEvent(input[[sprintf("currentGenomicRegion.%s", "igvShiny_0")]], {
newLoc <- input[[sprintf("currentGenomicRegion.%s", "igvShiny_0")]]
#observeEvent(input$genomicRegionChanged, {
#newLoc <- input$genomicRegionChanged
printf("new chromLocString: %s", newLoc)
output$chromLocDisplay <- renderText({newLoc})
})
genomes <- c("hg38", "hg19", "mm10", "tair10", "rhos")
loci <- c("chr5:88,466,402-89,135,305", "MEF2C", "Mef2c", "1:7,432,931-7,440,395", "NC_007494.2:370,757-378,078")
i <- 2
output$igvShiny_0 <- renderIgvShiny({
genomeOptions <- parseAndValidateGenomeSpec(genomeName=genomes[i], initialLocus=loci[i])
igvShiny(genomeOptions)
})
} # server
#----------------------------------------------------------------------------------------------------
print(sessionInfo())
server <- function(input, output, session){
callModule(igv_server, "igv")
}
ui <- fluidPage(
igv_ui(id="igv")
)
runApp(shinyApp(ui = ui, server = server), port=9834)
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