Class: intervals

LocusZoom_DataLayers~intervals()

(extension) Implements a data layer that will render interval annotation tracks (intervals must provide start and end values) Each interval (such as from a BED file) will be rendered as a rectangle. All spans can be rendered on the same row, or each (auto-detected) category can be rendered as one row per category.

This layer is intended to work with a variety of datasets with special requirements. As such, it has a lot of configuration options devoted to identifying how to fill in missing information (such as color)

Constructor

new intervals()

Parameters:
Name Type Attributes Default Description
layout.start_field string <optional>
 'start'

The field that defines interval start position
layout.end_field string <optional>
 'end'

The field that defines interval end position
layout.track_label_field string <optional>
 'state_name'

Used to label items on the y-axis
layout.track_split_field string <optional>
 'state_id'

Used to define categories on the y-axis. It is usually most convenient to use the same value for state_field and label_field (eg 1:1 correspondence).
layout.track_split_order * | 'DESC' <optional>
 'DESC'

When in split tracks mode, should categories be shown in the order given, or descending order
layout.track_split_legend_to_y_axis number <optional>
 2
layout.split_tracks boolean <optional>
 true

Whether to show tracks as merged (one row) or split (many rows) on initial render.
layout.track_height number <optional>
 15

The height of each interval rectangle, in px
layout.track_vertical_spacing number <optional>
 3
layout.bounding_box_padding number <optional>
 2
layout.always_hide_legend boolean <optional>
 false

Normally the legend is shown in merged mode and hidden in split mode. For datasets with a very large number of categories, it may make sense to hide the legend at all times.
layout.color string | Array.<module:LocusZoom_DataLayers~ScalableParameter> <optional>
 '#B8B8B8'

The color of each datum rectangle
layout.fill_opacity number | Array.<module:LocusZoom_DataLayers~ScalableParameter> <optional>
 1
layout.tooltip_positioning string <optional>
 'vertical'
Source:
See:

Methods

_arrangeTracksLinear()

Split data into rows using a simple greedy algorithm such that no two items overlap (share same interval) Assumes that the data are sorted so item1.start always <= item2.start.

This function can also simply return all data on a single row. This functionality may become configurable in the future but for now reflects a lack of clarity in the requirements/spec. The code to split overlapping items is present but may not see direct use.

Source:

getElementStatusNodeId() → {String}

When we are in "split tracks mode", it's convenient to wrap all individual annotations with a shared highlight box that wraps everything on that row.

This is done automatically by the "setElementStatus" code, if this function returns a non-null value

To define shared highlighting on the track split field define the status node id override to generate an ID common to the track when we're actively splitting data out to separate tracks

Source:
Returns:
Type
String