higlass-scalable-insets

Scalable Insets for HiGlass

Explore your beloved 2D annotations with Scalable Insets in HiGlass

Scalable Insets is a new technique for interactively exploring and navigating large numbers of annotated patterns in multiscale visual spaces such as gigapixel images, matrices, or maps. Our technique visualizes annotated patterns too small to be identifiable at certain zoom levels using insets, i.e., magnified thumbnail views of the patterns. Find out more at http://scalable-insets.lekschas.de and watch our <5min introductory video at https://youtu.be/7Bn4mNLl3WQ.

Note: This is the source code for the Scalable Insets tracks only! You might want to check out the following repositories as well if you want to know how Scalable Insets is integrated into HiGlass or use it with images or geographic maps:

• HiGlass viewer: https://github.com/hms-dbmi/higlass
• HiGlass server: https://github.com/hms-dbmi/higlass-server
• HiGlass image track: https://github.com/flekschas/higlass-image
• HiGlass GeoJSON track: https://github.com/flekschas/higlass-geojson

Installation

npm install higlass-scalable-insets

Usage

1. Make sure you load this track prior to hglib.js. For example:

<script src="higlass-scalable-insets.js"></script>
<script src="hglib.js"></script>
<script>
  ...
</script>

1. Configure the track in the view config.

{
  ...,
  tracks: {
    center: [
      {
        type: 'combined',
        options: {},
        contents: [
          // This tracks loads the Hi-C matrix
          {
            server: 'http://higlass.io/api/v1/',
            tilesetUid: 'CQMd6V_cRw6iCI_-Unl3PQ',  // Rao et al. 2014 GM12878
            type: 'heatmap',
          },
          // This track loads the annotated patterns
          {
              server: '//higlass.io/api/v1',
              tilesetUid: 'HunfK2D3R9iBdIq-YNYjiw',
              uid: 'anno-loops-1',
              type: '2d-rectangle-domains',
          },
          // This track is responsible for rendering the insets.
          {
            server: '//higlass.io/api/v1/',
            tilesetUid: 'CQMd6V_cRw6iCI_-Unl3PQ',
            uid: 'insets',
            type: 'insets',
            dataType: 'matrix',
          },
        ],
      },
    ],
    // You could also display the insets on the gallery of the matrix
    // gallery: {
    //   server: '//higlass.io/api/v1/',
    //   tilesetUid: 'CQMd6V_cRw6iCI_-Unl3PQ',
    //   type: 'insets',
    //   dataType: 'matrix',
    // },
    ...
  },
  metaTracks: {
    type: 'annotations-to-insets',
    insetsTrack: 'insets',
    options: {
      annotationTracks: ['ski-areas'],
    },
  }
}

Take a look at src/index.html for an example.

Configuration

Scalable Insets requires 2 tracks. An insets track, which handles the insets, and an annotations-to-insets track, which links all drawn annotations and compute the placement and clustering of insets.

Track: annotations-to-insets

Settings

Option	Type	Description
uid	str	Unique identifier.
type	str	Must be annotations-to-insets.
insetsTrack	str	UID of the insets track.

Options

The following options let you adjust the trade-off between Details, Context, and Locality. Please see the paper for details.

Option	Type	Default	Description
annotationTracks*	array of str	[]	Annotation tracks defining patterns.
boostContext	num	1	Higher boost means higher penalty for inset-context overlap (i.e., overlap of insets and other annotated regions).
boostDetails	num	1	Higher boost means higher penalty for inset-inset overlap.
boostLayout	num	1	Higher boost means more iteration cycles of the simulated annealing algorithm.
boostLayoutInit	num	1	Higher boost means more iteration cycles of the simulated annealing algorithm on start up.
boostLocality	num	1	Higher boost means higher penalty for distance between insets and their origin.
clusterAmong	str	None	Cluster only insets of the same type. Each type its own track.
disableClustering	bool	false	If true disables clustering of insets.
excludeTracks	array of str	[]	Annotation tracks which patterns should not be displayed as insets but which should still contribute to the placement of insets.
gridSize	int	48	Distance threshold from inset (or cluster) to another inset (or cluster) to determine whether both should be clustered.
insetThreshold	int	24	Minimum size (in pixels) of an annotation for which an inset should be displayed. I.e., if the annotation gets larger the inset is removed.
maxClusterDiameter	num	48	Maximum cluster diameter in projected pixel.
maxClusterSize	int	Infinity	Maximum cluster size by number of clustered insets.

*) Note This is the only mandatory option, I know it doesn't make sense semantically but it was the easiest way to implement given that HiGlass by default does not pass the entire track config to a track.

Track: insets

Settings

Option	Type	Description
server	str	URL from where the tileset should be loaded.
tilesetUid	str	UID of the tileset to explore.
uid	str	UID to identify this track. Needed by the annotations-to-insets track.
type	str	Must be insets.
chromInfoPath	str	URL to a chromosome info file.
dataType	str	Either cooler or image.
height	int	Height (or width) of the insets track if positioned as a gallery track. By default the height is 24px.

Options

Option	Type	Default	Description
aggregation	str	gallery	Aggregation mode. Options are gallery and pile.
borderColor	str	white	Color of the insets border and background. Color names and HEX are supported.
borderRadius	int	2	Border radius of the inset.
borderWidth	int	2	Border width of the inset.
colorRange	array of str	fall color map	Color map for rendering matrix insets.
dropBlur	num	3	Degree of blurring the drop shadow of insets.
dropDistance	num	1	Distance of the drop shadow of insets.
dropOpacity	num	0.8	Opacity of the drop shadow of insets.
focusColor	str	orange	"Focus color of insets, i.e., when mousing over an inset."
indicatorColor	str	black	Color of icons attached to the inset.
insetOriginPadding	int	6	Minimum distance between insets and their origin. Smaller distances will be penalized.
isFocusBorderOnScale	bool	true	If true change border color to focusColor upon scale up of an inset.
isIgnoreDiag	int	0	Number of diagonals to be ignored. Only applied to matrix insets.
isLogTransform	array of str	[]	List of annotation types which should be log transformed. Only applied to matrix insets.
leaderLineColor	str	white	Color of the leader line.
leaderLineDynamic	bool	false	If true leader line will update dynamically based on the cursor's distance to insets.
leaderLineDynamicMaxDist	num	256	Maximum distance from which onwards the leader line is most faded out.
leaderLineDynamicMinDist	num	12	Minimum distance from which onwards the leader line is most faded in.
leaderLineFading	bool	obj	false
leaderLineOpacity	num	1	Leader line opacity.
leaderLineStubLength	bool	num	false (if true then 12)
leaderLineStubWidth	int	2	Base width of the leader line stubs.
leaderLineStubWidthMax	int	2	Minimum width of leader line stubs.
leaderLineStubWidthMin	int	4	Maximum width of leader line stubs.
leaderLineWidth	int	2	Base leader line width in pixel.
loadHiResOnScaleUp	bool	false	If true load a higher resolution insets upon clicking on the inset.
maxPreviews	int	8	Maximum number of pile previews.
maxSize	int	16	Maximum inset size in pixels (not including the base scaling)
minSize	int	8	Minimum inset size in pixels (not including the base scaling)
onClickScale	num	2	Scale factor when clicking on an inset.
padding	int	0	"Relative padding for determining the zoom level when cutting out insets. E.g., 0.2 refers to 20% padding. Only regarded for matrix insets from cooler."
paddingCustom	obj	{}	"Key-value pairs for resolution-based padding for determining the zoom level. E.g., { 5000: 8, 10000: 4 } refers to 800% padding for resolutions of 5000 or lower. Only regarded for matrix insets from cooler."
paddingLoci	num	0	Location based padding for cutting out more than just the annotated pattern.
paddingLociCustom	obj	{}	"Key-value pairs defining resolution-based location padding. E.g., { 5000: 0.5, 10000: 0.25 } refers to 50% padding for resolutions of 5000 or lower."
pileOrientation	str	bottom	Where to display pile previews.
previewSize	int	4	Height of the previews in pixel. Only needed when matrix piles.
resolution	int	0	Default resolution. Only needed for matrix insets from cooler.
resolutionCustom	obj	{}
scale	int	3	Default scale factor of insets. Optimized for matrix insets from cooler.
scaleBorderBy	str	None	Can be any kind of inset property like 'clusterSize'.
scaleSizeBy	str	None	Can be any kind of inset property like 'clusterSize'.
selectColor	str	fuchsia	"Color name or HEX value for coloring the insets upon selection, i.e., when being scaled up."
sizeStepSize	int	2	Steps in pixel to increment the size of insets.

Development

Installation

$ git clone https://github.com/flekschas/higlass-scalable-insets && higlass-scalable-insets
$ npm install

Commands

Developmental server: npm start

Production build: npm run build

Co-Development with HiGlass

If you need to work on HiGlass and Scalable Insets in parallel I recommend the following setup:

1. Link a local HiGlass instance:

git clone https://github.com/hms-dbmi/higlass && cd higlass && npm install
npm link
npm run build

1. Open another terminal, link the HiGlass instance and start the web server

cd higlass-scalable-insets
npm link higlass
npm start

Now, whenever you make changes to your local HiGlass instance it will be re-build and also trigger a re-build of the Scalable Insets track.