library(shiny)
library(igvShiny)
library(htmlwidgets)
# library(biomaRt)
#----------------------------------------------------------------------------------------------------
data.directory <- system.file(package="igvShiny", "extdata", "sarsGenome")
fasta.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.dna.toplevel.fa")
fastaIndex.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai")
annotation.file <- file.path(data.directory, "Sars_cov_2.ASM985889v3.101.gff3")
title <- "SARS-CoV-2"
genomeOptions <- parseAndValidateGenomeSpec(genomeName=title,
initialLocus= NA,
stockGenome=FALSE,
dataMode="localFiles",
fasta=fasta.file,
fastaIndex=fastaIndex.file,
genomeAnnotation=annotation.file
)
#----------------------------------------------------------------------------------------------------
ui = shinyUI(fluidPage(
igvShinyOutput('igvShiny_0'),
))
#----------------------------------------------------------------------------------------------------
server = function(input, output, session) {
output$igvShiny_0 <- renderIgvShiny({
cat("--- starting renderIgvShiny\n");
x <- igvShiny(genomeOptions, displayMode="SQUISHED")
return(x)
})
} # server
#----------------------------------------------------------------------------------------------------
if(grepl("hagfish", Sys.info()[["nodename"]]) & !interactive()){
runApp(shinyApp(ui, server), port=6867)
} else {
shinyApp(ui, server)
}
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