v0.12.0-beta.1

Preview release that includes breaking changes

See #193 for details

v0.11.0

New features

• New coaccessibility loop visualization feature
• New tabix-reader extension
• New "guides" documentation for advanced layouts features
• New annotation feature allows users to preserve markings across rerender for custom code (eg "label this point")

Breaking changes

• Code cleanup and refactoring to support reuse
• Move non-generic features to extensions: Covariates Model dashboard widget, Intervals track

Bugfixes and other improvements

• Bugfixes for gene constraint and credible set display
• Improve LD point coloring when assoc data has a nonstandard variant format
• display_options widget can now control filter options, for data layers that support this
• Interval track now supports several ways to specify colors

0.10.2

Bugfix: improve how the gnomAD gene constraint source handles edge cases with unusual or duplicate gene names

0.10.1

• We have restored and improved gene constraint tooltips, using gnomAD as our new source of data. Using this feature on an existing site will require updating LocusZoom.Datasources options (see below). Tooltips now include o/e constraint metrics and confidence intervals. Genes with no constraint information now hide the table rather than showing blank fields.
  • Currently gene constraint information is only available for build GRCh37
• Fix a bug where panel titles were sometimes rendered twice

Breaking changes

• Old layouts using GeneConstraintLZ will need to be updated to use the new gnomAD API URL, as well as to correctly specify the genome build. For example: .add("constraint", ["GeneConstraintLZ", { url: "https://gnomad.broadinstitute.org/api", params: { build: 'GRCh37' } }]);
  • Although we generally try to preserve backwards compatibility, in this case, the old GeneConstraintLZ datasource was designed for a server (exAC) that is no longer available, and no custom datasources were found in an audit of users. Therefore the datasource has been redefined to use a different request and response format based on gnomAD.

0.10.0

New features

• New datalayer match directive allows users to click on a point, and see corresponding points with the same value on the same/other data layers. The visualization is based on existing configurable layout directives, providing control over point size, point shape, etc.
  • This is an experimental feature; the API and features may change based on user feedback
• Aggregation test demo now uses real data from a live server and supports more kinds of calculations
• Add a new widget to select LD population for the plot
  • All examples have been updated to add this widget
  • This widget is designed to work with the LDLZ2 data source, and the UMich LDServer at https://portaldev.sph.umich.edu/ld/ (prebuilt populations are based on those available in the 1000G dataset). We encourage all users to migrate off the old (legacy) LD API ( http://portaldev.sph.umich.edu/api/v1/pair/LD/results ), and enjoy new features made possible by the UMich LDServer.
  • This widget is not part of the default layout, because many old LZ installations are still using the old URL
• Dashboard widget improvements for developers
  • A new plot-level set_state dashboard widget lets users select an item from a menu to change plot.state. This can be used to modify requests dynamically- eg, to provide configuration options used to make LD requests
  • Developers can now control button text for the "Download" and "Resize to data" buttons
  • Developers can now specify a default filename other than 'locuszoom.svg" for the download image button

Bugfixes

• The "download plot as image" button is now faster and works more reliably when saving images of large (or dense) plot regions
• Default layouts and extensions will now more consistently apply the htmlescape filter for user-provided data
• Fix issues where closed tooltips could reopen when panning, zooming, or other dynamic actions
• "Full height" vertical lines will now redraw to the correct size when the plot is resized
• Fix regression where x-axis labels did not update to show region, when the plot was dynamically redrawn

Deprecations/ breaking changes

• The landing page for LocusZoom has been updated to emphasize CDNs. We no longer upload new versions of Locuszoom in a static asset folder on github; please migrate to using the CDN (or a build system like NPM + webpack) to get the newest code.
• The syntax for specifying color of phewas scatter plots has changed. Users of the stock layout should automatically be upgraded, but code for custom color schemes may need to be changed.
• All usages of the Q library have been replaced with native ES6 promises, including in the pre-bundled vendor.js. Custom code may need to be updated. In general this will involve small function renames.
  • locuszoom.vendor.js incorporates a polyfill for modern ES6 Promises, to help existing LocusZoom users ensure support for old browsers.
• Removed the "gene constraint information" table from gene track tooltips, due to lack of a data provider. This has been replaced with a link to gnomAD.
  • This change was made because the data source (exAC) has been decommissioned, and the new gnomAD API does not yet support bulk queries. We hope to restore this feature in the future.

0.10.0-beta.2

• Add a new widget to select LD population for the plot
  • All examples have been updated to add this widget
  • This widget is designed to work with the LDLZ2 data source, and the UMich LDServer (prebuilt populations are based on those available in the 1000G dataset). We encourage all users to migrate off the old (legacy) URL, and enjoy new features made possible by the UMich LDServer.
  • This widget is not part of the default layout, because many old LZ installations are still using the old URL
• Generic version: the LD picker uses the new plot-level set_state dashboard widget. This can be used to modify requests dynamically- eg, to provide configuration options used to make LD requests
• Fix regression where x-axis labels did not update to show region

0.10.0-beta.1

This is a preview release. It contains several minor, though possibly breaking, changes; we have posted it publicly to allow users try it out and give feedback.

New features

• New data-layer match directive allows users to click on a point, and see corresponding points with the same value on the same/other data layers. The visualization is based on existing configurable layout directives, providing control over point size, point shape, etc.
  • This is an experimental feature; the API and features may change based on user feedback
• Aggregation test demo now uses real data from a live server and support more kinds of calculations

Bugfixes

• The "download plot as image" button is now more reliable for large plot regions
• Default layouts and extensions will now more consistently apply the htmlescape filter for user-provided data

Deprecations/ breaking changes

• The landing page for LocusZoom has been updated to emphasize CDNs. We no longer upload new versions of Locuszoom in a static asset folder on github; please migrate to using the CDN (or a package manager like NPM) to get the newest code.
• The syntax for specifying color of phewas scatter plots has changed. Users of the stock layout should automatically be upgraded, but code for custom color schemes may need to be changed.
• All usages of the Q library have been replaced with native ES6 promises, including in the pre-bundled vendor.js. Custom code may need to be updated. In general this will involve small function renames.
  • Vendor JS incorporates a polyfill, to help existing LocusZoom users ensure support for old browsers.

0.9.1

• Bugfix: LD source will now correctly pick best variant for non-log pvalues
• Improve aggregation test demo to use real data from UM/METSIM LDServer
• Correctly support UMD module usage ; allows import 'LocusZoom'; for core + extensions
• Documentation fixes

(*) This was released to NPM May 2019, and has been retroactively tagged.

0.9.0

Summary

• New: configurable build 38 support for all datasources
• New: label SNPs in a study that are in the GWAS catalog
• Improve reusability and caching for credible set calculations
• Forest plots have better support for handling dynamic data
• Annotation/rug tracks are easier to click, and have a configurable tooltip position.
• Line track now supports filled curves
• Plots now support a "width_only" responsive resize mode. This is useful for dynamic layouts or rug tracks (where more control over panel height is desired)
• The display_options widget has improved control over legends and item labels
• Improvements for development and debugging
  • Many error messages now log debugging stacktraces to the console
  • Issue console warnings for certain behaviors known to cause broken layouts
• New plot level event: notify when a panel is removed.
• Label and element filtering options now support != to test for absence of a value.

Developer notes

Deprecation warnings

• The original LD Source (LDLZ) is now deprecated. All examples have been upgraded to use LDLZ2, which uses the new Michigan LDServer.
  • The new source supports multiple genome builds and configurable choice of reference panels; the previous LD source does not offer this functionality, and relies on a deprecated server endpoint.
• The plot builder tool was unmaintained, and has been removed.
• vendor.js has been updated to use a slightly newer d3 version. (3.5.6 --> 3.5.17)

Features and layout changes

• Where possible, most "region" data sources (genes, recomb rate, and LD) will respond to a state.genome_build parameter, and automatically attempt to select the best API source for that build.
  • params.source parameter is no longer required for many data sources. To ensure that your plot uses the newest and best version of data available, we recommend using params.build or state.genome_build instead.

Bugfixes

• Better handling for regions with no data

0.8.2

Allow forest plots to operate on dynamic data from the server

New category_forest layer type that allows ticks and labels to be
determined from the server response, without having to be specified
in the layout in advance

Updated forest plot example to take advantage of these features.