A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.
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README.md

LocusZoom

LocusZoom is a Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

Build Status

See github.com/statgen/locuszoom/wiki for full documentation and API reference.

To see functional examples of plots generated with LocusZoom.js see statgen.github.io/locuszoom and statgen.github.io/locuszoom/#examples.

LocusZoom.js Standard Association Plot (v0.5.2)

Making a LocusZoom Plot

1. Include Necessary JavaScript and CSS

The page you build that embeds the LocusZoom plugin must include the following resources, found in the dist directory:

  • locuszoom.vendor.min.js
    This file contains the concatenated vendor libraries. You can alternatively include d3 and Q from other sources, so long as they are included before including LocusZoom files.

  • locuszoom.app.js OR locuszoom.app.min.js
    This is the primary application logic. It should only be included after the vendor dependencies have been included.

  • locuszoom.css
    This is the primary stylesheet. It is namespaced so as not to conflict with any other styles defined on the same page.

CDN links are available for these resources (see statgen.github.io/locuszoom/).

2. Define Data Sources

Data Sources is an object representing a collection of arbitrarily many sources from which data for the plot can be requested. When adding sources to the collection they must be namespaced so that retrieving specific fields can be done with respect to specific data sources.

Here's an example of defining a data sources object for a remote API:

var data_sources = new LocusZoom.DataSources();
data_sources.add("trait", ["AssociationLZ", { url: "http://server.com/api/" }]);

The above example adds an "AssociationLZ" data source (a predefined data source designed to make requests for association data) with a defined URL. The namespace for this data source is "trait".

Data sources can also be local files:

data_sources = new LocusZoom.DataSources();
data_sources.add("trait", ["AssociationLZ", { url: "file:///path/to/data.json" }]);

Refer to the Data Sources Documentation for more information on using predefined data sources or extending/creating custom data sources.

3. Define a Layout

Layout is a serializable object that describes the configuration of the LocusZoom plot, including what data will be pulled from the data sources and displayed in what way, along with visual characteristics like color and geometry.

A layout definition may look something like this:

var layout = {
  width: 500,
  height: 500,
  panels: [
    {
      id: "association",
      data_layers: [
         {
           id: "association",
           type: "scatter",
           fields: ["trait:position", "trait:pvalue"],
           x_axis: { field: "trait:position" },
           y_axis: { field: "trait:pvalue" }
         }
      ]
    }
  ]
};

The above example defines a basic plot that is 500 pixels on a side and has one panel with one scatter plot data layer that pulls in position and pvalue from the "trait" data source, mapping position to the x axis and pvalue to the y axis.

The LocusZoom.js library provides several pre-defined layouts for entire plots and subdivisions of plots such as panels, data layers, tool tips, etc. Refer to the Layout Documentation for more information.

4. Put it Together with LocusZoom.populate()

With includes included, data sources defined, and a layout defined, LocusZoom.populate() will accept a CSS selector string to populate the first matching element with a plot.

A basic example may then look like this:

<html>
  <head>
    <script src="locuszoom.vendor.min.js" type="text/javascript"></script>
    <script src="locuszoom.app.js" type="text/javascript"></script>
    <link rel="stylesheet" type="text/css" href="locuszoom.css"/>
  </head>
  <body>
    <div id="plot"></div>
    <script type="text/javascript">
      var data_sources = new LocusZoom.DataSources();
      data_sources.add("trait", ["AssociationLZ", { url: "http://server.com/api/single/" }]);
      var layout = {
        width: 500,
        height: 500,
        panels: [
          {
            id : "association",
            data_layers: [
              {
                id: "association",
                type: "scatter",
                fields: ["trait:position", "trait:pvalue"],
                x_axis: { field: "trait:position" },
                y_axis: { field: "trait:pvalue" }
              }
            ]
          }
        ]
      };
      var plot = LocusZoom.populate("#plot", data_sources, layout);
    </script>
  </body>
</html>

Other Ways To Make a LocusZoom Plot

Use a Predefined Layout

The core LocusZoom library comes equipped with several predefined layouts, organized by type ("plot", "panel", "data_layer", and "dashboard"). You can see what layouts are predefined by reading the contents of assets/js/app/Layouts.js or in the browser by entering LocusZoom.Layouts.list() (or to list one specific type: LocusZoom.Layouts.list(type)).

Get any predefined layout by type and name using LocusZoom.Layouts.get(type, name).

If no layout is passed to LocusZoom.populate() the Standard GWAS plot layout is used (requiring appropriate data sources to be configured).

Build a Layout Using Some Predefined Pieces

LocusZoom.Layouts.get(type, name) can also be used to pull predefined layouts of smaller pieces, like data layers or dashboards, into a custom layout:

var layout = {
  width: 1000,
  height: 500,
  panels: [
    LocusZoom.Layouts.get("panel","gwas"),
    {
      id: "custom_panel",
      ...
    },
    LocusZoom.Layouts.get("panel","genes")
  ]
  ...
};

Modify a Predefined Layout

The get() function also accepts a partial layout to be merged with the predefined layout as a third argument, providing the ability to use predefined layouts as starting points for custom layouts with only minor differences. Example:

var changes = {
  label_font_size: 20,
  transition: false
};
LocusZoom.Layouts.get("data_layer", "genes", changes);

Predefining State by Building a State Object

State is a serializable JSON object that describes orientation to specific data from data sources, and specific interactions with the layout. This can include a specific query against various data sources or pre-selecting specific elements. Essentially, the state object is what tracks these types of user input under the hood in LocusZoom, and it can be predefined at initialization as a top-level parameter in the layout. For example:

var layout = LocusZoom.Layouts.merge({ state: { chr: 6, start: 20379709, end: 20979709 } }, LocusZoom.StandardLayout);

Predefining State With data-region

You can also describe the locus query aspect of the State (chromosome, start, and end position) using a data-region attribute of the containing element before populating it, like so:

<div id="foo" data-region="10:114550452-115067678"></div>

When LocusZoom.populate() is executed on the element defined above it will automatically parse any data-region parameter to convert those values into the initial state.

Making Many LocusZoom Plots at Once

LocusZoom.populate() will only populate the first matching HTML element for the provided selector string. To populate all matching elements for a single selector string use LocusZoom.populateAll() like so:

<div class="plot" id="plot_1"></div>
<div class="plot" id="plot_2"></div>
<div class="plot" id="plot_3"></div>
<script type="text/javascript">
  var plots[] = LocusZoom.populateAll(".plot", data_source, layout);
</script>

Development Setup

Dependencies

LocusZoom is an entirely client-side application designed to plug into arbitrary data sets, be they local files, APIs, or something else entirely. It has the following vendor dependencies:

  • d3 for a data visualization framework
  • Q for a promises framework

Build System and Automated Testing

The application is built using Gulp. Gulp and all necessary dev dependencies can be installed for this project from the top-level directory using the following commands:

$ sudo npm install gulp-cli -g    # If you don't already have gulp-cli installed globally
$ npm install

Once complete run gulp from the top of the application directory to run all tests and build the following files (in the dist folder):

  • locuszoom.app.js - A concatenated app file suitable for use in development
  • locuszoom.app.min.js - A concatenated and minified app file suitable for use in production
  • locuszoom.vendor.min.js - A concatenated vendor file suitable for use as a single vendor include in either development or production (contains d3 and Q)
  • locuszoom.css - A generated CSS file for all LocusZoom styles

This build process will also write sourcemaps, to help with debugging code even in production environments.

Other supported gulp commands:

  • gulp watch - Watch for any changes to app .js, .scss, or test source files to trigger another full build
  • gulp test - Just run the tests
  • gulp js - Build app and vendor js files (runs tests and aborts if tests fail)
  • gulp app_js - Build app js files (runs tests and aborts if tests fail)
  • gulp vendor_js - Build vendor js file
  • gulp css - Build CSS file

The --force Flag

Append --force to the end of any gulp command that runs the automated testing suite to force the creation of locuszoom.app.js and locuszoom.app.min.js even when the tests fail. This can be useful during active development as sometimes debugging can be led from either the output of automated tests or inspection of an active plugin.

This flag is particularly useful with the watch command:

$ gulp watch --force

The above command with enter forced-watch-mode, which will detect any changes to app .js or .scss files, as well as test files, and run a new build. If errors are encountered in the tests they will be reported, but locuszoom.app.js and locuszoom.app.min.js will still be generated and gulp will not exit but return to watch mode. This is an effective way to have automatic continuous builds while developing both the application and its tests.

Automated Testing

LocusZoom uses Mocha for unit testing. Tests are located in the test subdirectory, with a one-to-one mapping of test files to app files.

Note that the build and test process requires Node.js version 6 LTS or higher.

Linting and Strict Mode

All app-specific javascript files should be developed in strict mode. LocusZoom is also linted using ESLint, the rules for which can be found in .eslintrc.

Help and Support

Full documentation can be found here: github.com/statgen/locuszoom/wiki

A LocusZoom discussion forum is available here: groups.google.com/forum/#!forum/locuszoom

If you have questions or feedback please file an issue on the LocusZoom.js GitHub repository or post at the discussion forum referenced above.