Global

Methods

clone(data) → {*}

The "just-clone" library only really works for objects and arrays. If given a string, it would mess things up quite a lot.

Parameters:
Name Type Description
data object
Source:
Returns:
Type
*

getLinkedData(shared_options, entities, dependencies, consolidateopt) → {Promise.<Array.<Object>>}

Perform a request for data from a set of providers, taking into account dependencies between requests. This can be a mix of network requests or other actions (like join tasks), provided that the provider be some object that implements a method instance.getData

Each data layer in LocusZoom will translate the internal configuration into a format used by this function. This function is never called directly in custom user code. In locuszoom, Requester Handles You

TODO Future: It would be great to add a warning if the final element in the DAG does not reference all dependencies. This is a limitation of the current toposort library we use.

Parameters:
Name Type Attributes Default Description
shared_options object

Options passed globally to all requests. In LocusZoom, this is often a copy of "plot.state"
entities Map

A lookup of named entities that implement the method instance.getData -> Promise
dependencies Array.<String>

A description of how to fetch entities, and what they depend on, like ['assoc', 'ld(assoc)']. Order will be determined by a DAG and the last item in the DAG is all that is returned.
consolidate boolean <optional>
 true

Whether to return all results (almost never used), or just the last item in the resolved DAG. This can be a pitfall in common usage: if you forget a "join/consolidate" task, the last result may appear to be missing some data.
Source:
Returns:
Type
Promise.<Array.<Object>>

Type Definitions

eventCallback(eventData)

Parameters:
Name Type Description
eventData object

A description of the event

Properties
Name Type Description
sourceID String | null

The unique identifier (eg plot or parent name) of the element that triggered the event. Will be automatically filled in if not explicitly provided.
context Object | null

Any additional information to be passed to the callback, eg the data associated with a clicked plot element
Source:

externalDataCallback(new_data, plot)

A user-defined callback function that can receive (and potentially act on) new plot data.

Parameters:
Name Type Description
new_data Object

The body resulting from a data request. This represents the same information that would be passed to a data layer making an equivalent request.
plot Object

A reference to the plot object. This can be useful for listeners that react to the structure of the data, instead of just displaying something.
Source:

externalErrorCallback(err)

A user-defined callback function that can respond to errors received during a previous operation

Parameters:
Name Type Description
err

A representation of the error that occurred
Source:

Events

any_lz_event

Fields common to every event emitted by LocusZoom. This is not an actual event that should ever be used directly; see list below.

Note: plot-level listeners can be defined for this event, but you should almost never do this. Use the most specific event name to describe the thing you are interested in.

Listening to 'any_lz_event' is only for advanced usages, such as proxying (repeating) LZ behavior to a piece of wrapper code. One example is converting all LocusZoom events to vue.js events.

Type:
  • object
Properties:
Name Type Description
sourceID string

The fully qualified ID of the entity that originated the event, eg lz-plot.association
target Plot | Panel

A reference to the plot or panel instance that originated the event.
data object | null

Additional data provided. (see event-specific documentation)
Source:

data_from_layer

One particular data layer has completed a request for data. This event is primarily used internally by the subscribeToData function, and the syntax may change in the future.

Properties:
Name Type Description
data object
Properties
Name Type Description
layer String

The fully qualified ID of the layer emitting this event
content Array.<Object>

The data used to draw this layer: an array where each element represents one row/ datum element. It reflects all namespaces and data operations used by that layer.
Source:
See:
Listeners of This Event:

data_rendered

A request for new data has completed, and all data has been rendered in the plot.

Source:
See:
Listeners of This Event:

data_requested

A request for new or cached data was initiated. This can be used for, eg, showing data loading indicators.

Source:
See:
Listeners of This Event:

element_clicked

Indicates whether an element was clicked. (regardless of the behavior associated with clicking)

Source:
See:

element_selection

Indicate whether the element was selected (or unselected)

Properties:
Name Type Description
data object

An object with keys { element, active }, representing the datum bound to the element and the selection status (boolean)
Source:
See:

layout_changed

An action occurred that changed, or could change, the layout. Many rerendering operations can fire this event and it is somewhat generic: it includes resize, highlight, and rerender on new data. Caution: Direct layout mutations might not be captured by this event. It is deprecated due to its limited utility.

Deprecated:
  • Yes
Source:
See:

match_requested

Indicate whether a match was requested from within a data layer.

Properties:
Name Type Description
data object

An object of {value, active} representing the scalar value to be matched and whether a match is being initiated or canceled
Source:
See:
Listeners of This Event:

panel_removed

A panel was removed from the plot. Commonly initiated by the "remove panel" toolbar widget.

Properties:
Name Type Description
data string

The id of the panel that was removed (eg 'genes')
Source:
See:

region_changed

The plot region has changed. Reports the actual coordinates of the plot after the zoom event. If plot.applyState is called with an invalid region (eg zooming in or out too far), this reports the actual final coordinates, not what was requested. The actual coordinates are subject to region min/max, etc.

Properties:
Name Type Description
data object

The {chr, start, end} coordinates of the requested region.
Source:
See:

set_ldrefvar

A new LD reference variant has been selected (usually by clicking within a GWAS scatter plot) This event only fires for manually selected variants. It does not fire if the LD reference variant is automatically selected (eg by choosing the most significant hit in the region)

Properties:
Name Type Description
data object

{ ldrefvar } The variant identifier of the LD reference variant
Source:
See:

state_changed

The user has requested any state changes, eg via plot.applyState. This reports the original requested values even if they are overridden by plot logic. Only triggered when a state change causes a re-render.

Properties:
Name Type Description
data object

The set of all state changes requested
Source:
See:
Listeners of This Event: