Nothing
## ----echo=FALSE, include=FALSE------------------------------------------------
knitr::opts_chunk$set(eval = FALSE)
## -----------------------------------------------------------------------------
# library(shiny)
# library(JBrowseR)
#
# ui <- fluidPage()
#
# server <- function(input, output, session) {}
#
# shinyApp(ui, server)
## -----------------------------------------------------------------------------
# ui <- fluidPage(
# titlePanel("Sars-CoV-2 JBrowseR Example"),
# # this adds to the browser to the UI, and specifies the output ID in the server
# JBrowseROutput("browserOutput")
# )
#
# server <- function(input, output, session) {
# # create the necessary JB2 assembly configuration
# assembly <- assembly(
# "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz",
# bgzip = TRUE
# )
#
# # link the UI with the browser widget
# output$browserOutput <- renderJBrowseR(
# JBrowseR(
# "View",
# assembly = assembly
# )
# )
# }
#
# shinyApp(ui, server)
## -----------------------------------------------------------------------------
# server <- function(input, output, session) {
# # create the necessary JB2 assembly configuration
# assembly <- assembly(
# "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz",
# bgzip = TRUE
# )
#
# # create configuration for a JB2 GFF FeatureTrack
# annotations_track <- track_feature(
# "https://jbrowse.org/genomes/sars-cov2/sars-cov2-annotations.sorted.gff.gz",
# assembly
# )
#
# # create the tracks array to pass to browser
# tracks <- tracks(annotations_track)
#
# # link the UI with the browser widget
# output$browserOutput <- renderJBrowseR(
# JBrowseR(
# "View",
# assembly = assembly,
# # pass our tracks here
# tracks = tracks
# )
# )
# }
## -----------------------------------------------------------------------------
# tracks <- tracks(
# annotations,
# variants,
# alignments
# )
## -----------------------------------------------------------------------------
# # set up the default session for the browser
# default_session <- default_session(
# assembly,
# c(annotations_track)
# )
## -----------------------------------------------------------------------------
# output$browserOutput <- renderJBrowseR(
# JBrowseR(
# "View",
# assembly = assembly,
# tracks = tracks,
# location = "NC_045512.2:1..100",
# defaultSession = default_session
# )
# )
## -----------------------------------------------------------------------------
# # accepts up to four colors for creating a custom palette
# theme <- theme("#5da8a3", "#333")
## -----------------------------------------------------------------------------
# output$browserOutput <- renderJBrowseR(
# JBrowseR(
# "View",
# assembly = assembly,
# tracks = tracks,
# location = "NC_045512.2:1..100",
# defaultSession = default_session,
# theme = theme
# )
# )
## -----------------------------------------------------------------------------
# ui <- fluidPage(
# titlePanel("Sars-CoV-2 JBrowseR Example"),
# # this adds to the browser to the UI, and specifies the output ID in the server
# JBrowseROutput("browserOutput")
# )
#
# server <- function(input, output, session) {
# # create the necessary JB2 assembly configuration
# assembly <- assembly(
# "https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz",
# bgzip = TRUE
# )
#
# # create configuration for a JB2 GFF FeatureTrack
# annotations_track <- track_feature(
# "https://jbrowse.org/genomes/sars-cov2/sars-cov2-annotations.sorted.gff.gz",
# assembly
# )
#
# # create the tracks array to pass to browser
# tracks <- tracks(
# annotations_track
# )
#
# # set up the default session for the browser
# default_session <- default_session(
# assembly,
# c(annotations_track)
# )
#
# theme <- theme("#5da8a3", "#333")
#
# # link the UI with the browser widget
# output$browserOutput <- renderJBrowseR(
# JBrowseR(
# "View",
# assembly = assembly,
# tracks = tracks,
# location = "NC_045512.2:1..100",
# defaultSession = default_session,
# theme = theme
# )
# )
# }
#
# shinyApp(ui, server)
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