A {shiny} app to wrap BlasterJS and visualize NCBI blast results locally

Shiny
R
blasterjs
NCBI
BLAST
Author

teo

Published

2022-06-23

blast and BlasterJS

I recently learned about a really slick JavaScript component for interactive visualization of NCBI’s blast output. BlasterJS (Website, Paper) makes it possible to visualize blast results in a way similar to the typical viz available on NCBI’s website. This is a fantastic resource, both in a day-to-day bioinformatics workflows, as well as for sharing results of genomics projects. For example, if we sequenced a novel genome and would like our collaborators or the public to blast some sequences against our genome, we could show the results with BlasterJS. Awesome!

BlasterJS dependencies and HTML template

Being an R programmer, and considering the wealth of Bioconductor resources for bioinformatics, I thought being able to run BlasterJS from R would be very useful. So I wrote a very small and simple {golem} application, called {blastR} to launch BlasterJS from R. One can install the {blastR} package locally and launch it when needed, or deploy an instance of blastR on their favorite {shiny} server platform to simply upload a blast output file.

With {golem}, the steps to make BlasterJS available in shiny are super easy:

  1. Download the JavaScript dependencies (blaster.js and html2canvas.js) and place them inst/app/www/js. inst/app/www is the typical path for adding external resources to {shiny}, and is added to the resource path by {golem} by default. We also add another subdirectory, js, because the BlasterJS HTML template expect these resources in a folder called js.

(The BlasterJS website also mentions Bootstrap 3 as a dependency, but we don’t need to load that as it is bundled with {shiny} already.)

  1. Create a {shiny} HTML template from the suggested BlasterJS HTML template. With {golem}, this is as easy as:
golem::add_html_template("BlasterJS")
#>  ✔ File created at /home/blasteR/inst/app/www/BlasterJS.html
#>  
#>  ── To use this html file as a template, add the following code in app_ui.R: ──────────────────────────────────
#>  htmlTemplate(
#>      app_sys("app/www/BlasterJS.html"),
#>      body = tagList()
#>      # add here other template arguments
#>  )

Then, we navigate to “inst/app/www/” and open “BlasterJS.html”. Copy the HTML suggested by the BlasterJS team:

<head>
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous" />
    ...
</head>
<body>
    ...
    <input type="file" id="blastinput" />
    <div id="blast-multiple-alignments"></div>
    <div id="blast-alignments-table"></div>
    <div id="blast-single-alignment"></div>
    ...
    <script type="text/javascript" src="js/html2canvas.js"></script>
    <script type="text/javascript" src="js/blaster.js"></script>
    <script type="text/javascript">
        var blasterjs = require("biojs-vis-blasterjs");
        var instance  = new blasterjs({
            input: "blastinput",
            multipleAlignments: "blast-multiple-alignments",
            alignmentsTable: "blast-alignments-table",
            singleAlignment: "blast-single-alignment"
        });    
    </script>
</body>

And modify:
1. To remove the head tag, this will come from our {shiny} app HTML.
2. Change the <body></body> container into a plain <div></div> container.
(This is probably not necessary, but it makes more sense to insert this HTML as a div, not the whole body of our {shiny} app)

After these changes, the contents of inst/app/www/BlasterJS.html should be:

<div>
    <input type="file" id="blastinput" />
    <div id="blast-multiple-alignments"></div>
    <div id="blast-alignments-table"></div>
    <div id="blast-single-alignment"></div>
    <script type="text/javascript" src="js/html2canvas.js"></script>
    <script type="text/javascript" src="js/blaster.js"></script>
    <script type="text/javascript">
        var blasterjs = require("biojs-vis-blasterjs");
        var instance  = new blasterjs({
            input: "blastinput",
            multipleAlignments: "blast-multiple-alignments",
            alignmentsTable: "blast-alignments-table",
            singleAlignment: "blast-single-alignment"
        });
    </script>
</div>

A {shiny} + {golem} application wrapping BlasterJS

Finally, to use this HTML template, we write in our app_ui:

app_ui <- function(request) {
  tagList(
    golem_add_external_resources(),
    fluidPage(
      h1("blasteR: A shiny app using the wonderful `BlasterJS` component"),
      shiny::htmlTemplate(app_sys("app/www/BlasterJS.html"))
    )
  )
}

Done!