## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("igvShiny") ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(igvShiny) ## ----eval=FALSE--------------------------------------------------------------- # library(igvShiny) # options <- parseAndValidateGenomeSpec(genomeName="hg38", initialLocus="NDUFS2") # if (interactive()) { # ui <- shinyUI(fluidPage(igvShinyOutput('igvShiny'), width = 10)) # server <- # function(input, output, session) { # output$igvShiny <- renderIgvShiny({ # igvShiny(options) # }) # } # runApp(shinyApp(ui = ui, server = server)) # } ## ----echo=TRUE---------------------------------------------------------------- igvShiny::parseAndValidateGenomeSpec("mm10") ## ----echo=TRUE---------------------------------------------------------------- igvShiny::get_css_genomes() ## ----echo=TRUE---------------------------------------------------------------- library(igvShiny) demo_app_file <- system.file(package= "igvShiny", "demos", "stockGenomesDemo.R") if (interactive()) { shiny::runApp(demo_app_file) } ## ----echo=TRUE---------------------------------------------------------------- library(igvShiny) # defining custom genome with data provided via URLs base_url <- "https://gladki.pl/igvr/testFiles" title <- "ribo remote" fasta_file <- sprintf("%s/%s", base_url, "ribosomal-RNA-gene.fasta") fastaIndex_file <- sprintf("%s/%s", base_url, "ribosomal-RNA-gene.fasta.fai") annotation_file <- sprintf("%s/%s", base_url, "ribosomal-RNA-gene.gff3") locus <- "U13369.1:7,276-8,225" genomeOptions <- parseAndValidateGenomeSpec( genomeName = title, initialLocus = locus, stockGenome = FALSE, dataMode = "http", fasta = fasta_file, fastaIndex = fastaIndex_file, genomeAnnotation = annotation_file ) genomeOptions # defining custom genome with data provided with local files data_directory <- system.file(package = "igvShiny", "extdata") fasta_file <- file.path(data_directory, "ribosomal-RNA-gene.fasta") fastaIndex_file <- file.path(data_directory, "ribosomal-RNA-gene.fasta.fai") annotation_file <- file.path(data_directory, "ribosomal-RNA-gene.gff3") genomeOptions2 <- parseAndValidateGenomeSpec( genomeName = "ribo local", initialLocus = "U13369.1:7,276-8,225", stockGenome = FALSE, dataMode = "localFiles", fasta = fasta_file, fastaIndex = fastaIndex_file, genomeAnnotation = annotation_file ) genomeOptions2 ## ----echo=TRUE---------------------------------------------------------------- library(igvShiny) demo_app_file <- system.file( package = "igvShiny", "demos", "igvShinyDemo-customGenome-http.R" ) if (interactive()) { shiny::runApp(demo_app_file) } ## ----echo=TRUE---------------------------------------------------------------- library(igvShiny) demo_app_file <- system.file( package = "igvShiny", "demos", "igvShinyDemo-customGenome-localFiles.R") if (interactive()) { shiny::runApp(demo_app_file) } ## ----echo=TRUE---------------------------------------------------------------- library(igvShiny) demo_app_file <- system.file(package= "igvShiny", "demos", "igvShinyDemo.R") if (interactive()) { shiny::runApp(demo_app_file) } ## ----------------------------------------------------------------------------- sessionInfo()