# Custom browser tutorial

This tutorial will cover how to embed JBrowseR into a shiny app, and how to customize the browser by creating data tracks and a custom theme. Before we get started with writing R code, it is necessary to cover some JBrowse 2 concepts, and look at how to prepare data for use with the browser. There are three core aspects of JBrowse 2 configuration:

- Assembly: the reference assembly being displayed
- Tracks: the generic container for displaying various types of genomic data in the browser
- defaultSession: what is displayed when the browser is first loaded

Other import points of configuration are the location, which is the location in the genome on first load, and the theme, which can be used to create a custom color palette for your browser. While all of these values are possible, the only required configuration is an assembly.

## Preparing an assembly

The steps for preparing an assembly for use in the browser can be found in the JBrowse 2 docs, but we will cover them again here. In order to be used, an assembly must first be indexed. We will be using the Sars-CoV-2 genome for this tutorial.

To create an index, we first need to download the FASTA for the assembly. This can be found here. We also need htslib, which provides the tools we need for indexing and compression. (I prefer to install htslib using bioconda). The remaining steps assume the htslib is installed, and we have a fasta file named `sars-cov2.fa`.

With these steps taken, we are going to compress and index the assembly, for best performance. The necessary commands are:

    # 1. compresses sars-cov2.fa to sars-cov2.fa.gz
    # 2. generates sars-cov2.fa.gz.fai and sars-cov2.fa.gz.gzi
    bgzip sars-cov2.fa
    samtools faidx sars-cov2.fa.gz

For the rest of the tutorial code, we are going to use the following already hosted results of these commands:

- `https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz`
- `https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.fai`
- `https://jbrowse.org/genomes/sars-cov2/fasta/sars-cov2.fa.gz.gzi`

However, these are the same steps for preparing any assembly for use with the browser. For notes on creating URLs for your data either locally or hosted, read more here.

## Creating a minimal shiny app

Shiny is an excellent web framework that makes it easy to create interactive web applications with a minimal amount of R code. The basic Shiny app consists of a UI and a server:

    library(shiny)
    library(JBrowseR)

    ui <- fluidPage()

    server <- function(input, output, session) {}

    shinyApp(ui, server)

This is all of the boilerplate code we need for our app. Now, we can add the browser displaying the Sars-CoV-2 genome.

    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)

That is all of the code we need to add a custom genome browser to a Shiny app! It is worth noting that the `assembly()` function takes only the root FASTA file as the argument, but infers the `.fai` and `.gzi` files because they use the standard naming convention. A similar pattern is true for other tracks that require index files. In these cases, it is noted in the function documentation.

## Adding tracks

With an embedded browser running in a Shiny app, we can look at how to add data tracks to the browser. Adding tracks takes place in the server function:

    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
        )
      )
    }

JBrowseR has functions for adding four track types:

- `track_alignments()`: visualize BAM or CRAM alignment data
- `track_feature()`: visualize GFF3 data
- `track_variant()`: visualize VCF data
- `track_wiggle()`: visualize bigWig data

Any number of tracks can be passed to the main tracks function, for example:

    tracks <- tracks(
      annotations,
      variants,
      alignments
    )

but for now, we will stick with the feature track that we’ve created.

## Setting a default session

Up until this point, nothing is displayed by default in the browser when the app first loads. We can change that by configuring the default session:

    # set up the default session for the browser
    default_session <- default_session(
      assembly,
      c(annotations_track)
    )

This sets up the browser to display the reference track and the annotations track by default when it loads.

Now we update the call to our renderer:

    output$browserOutput <- renderJBrowseR(
        JBrowseR(
          "View",
          assembly = assembly,
          tracks = tracks,
          location = "NC_045512.2:1..100",
          defaultSession = default_session
        )
    )

Here we have passed the `default_session` we created, and set a starting location for the browser (the first 100 bases).

## Creating a custom theme

In addition to visualizing your own data, you may want your browser to have your own theme. Another JBrowseR function makes creating a custom theme very simple:

    # accepts up to four colors for creating a custom palette
    theme <- theme("#5da8a3", "#333")

And again we update the renderer, now passing the theme:

    output$browserOutput <- renderJBrowseR(
        JBrowseR(
          "View",
          assembly = assembly,
          tracks = tracks,
          location = "NC_045512.2:1..100",
          defaultSession = default_session,
          theme = theme
        )
    )

## Putting it all together

Let’s take a look at the final complete app:

    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)

Awesome, we’ve added a genome browser with annotations and a custom theme to a Shiny app!