Class: genes

LocusZoom_DataLayers~genes()

Genes Data Layer Implements a data layer that will render gene tracks

Constructor

new genes()

Parameters:
Name Type Attributes Default Description
layout.stroke string | Array.<module:LocusZoom_DataLayers~ScalableParameter> <optional>
'rgb(54, 54, 150)'

The stroke color for each intron and exon

layout.color string | Array.<module:LocusZoom_DataLayers~ScalableParameter> <optional>
'#363696'

The fill color for each intron and exon

layout.label_font_size number <optional>
layout.label_exon_spacing number <optional>

The number of px padding between exons and the gene label

layout.exon_height number <optional>
10

The height of each exon (vertical line) when drawing the gene

layout.bounding_box_padding number <optional>
3

Padding around edges of the bounding box, as shown when highlighting a selected gene

layout.track_vertical_spacing number <optional>
5

Vertical spacing between each row of genes

layout.tooltip_positioning 'horizontal' | 'vertical' | 'top' | 'bottom' | 'left' | 'right' <optional>
'top'

Where to draw the tooltip relative to the datum.

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See:

Members

(static, constant) default_layout :Object

Type:
  • Object
Source:

gene_track_index :Object.<Number, Array>

Store information about genes in dataset, in a hash indexed by track number: {track_number: [gene_indices]}

Type:
  • Object.<Number, Array>
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(protected) tracks :number

An internal counter for the number of tracks in the data layer. Used as an internal counter for looping over positions / assignments

Type:
  • number
Source:

transcript_idx :number

A gene may have arbitrarily many transcripts, but this data layer isn't set up to render them yet. Stash a transcript_idx to point to the first transcript and use that for all transcript refs.

Type:
  • number
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Methods

assignTracks() → {Genes}

Ensure that genes in overlapping chromosome regions are positioned so that parts of different genes do not overlap in the view. A track is a row used to vertically separate overlapping genes.

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Returns:
Type
Genes

getElementStatusNodeId() → {String}

Generate a statusnode ID for a given element

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Returns:
Type
String

getTrackHeight() → {number}

Helper function to sum layout values to derive total height for a single gene track

Source:
Returns:
Type
number

render()

Main render function

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