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Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info

Source file


DotplotRenderer - Slots

slot: color

color: {
type: 'color',
'the color of each feature in a synteny, used with colorBy:default',
defaultValue: '#f0f',
contextVariable: ['feature'],

slot: posColor

posColor: {
type: 'color',
description: 'the color for forward alignments, used with colorBy:strand',
defaultValue: 'blue',

slot: negColor

negColor: {
type: 'color',
description: 'the color for reverse alignments, used with colorBy:strand',
defaultValue: 'red',

slot: lineWidth

lineWidth: {
type: 'number',
description: 'width of the lines to be drawn',
defaultValue: 2.5,

slot: colorBy

colorBy: {
type: 'stringEnum',
model: types.enumeration('colorBy', [
description: `Color by options:<br/>
<li>"identity" - the identity of the particular hit, similar to D-GENIES, use the other config slots 'thresholds' and 'thresholdsPalette' to define colors for this setting</li>
<li>"meanQueryIdentity" - calculates the weighted mean identity (weighted by alignment length) of all the hits that the query maps to (e.g. if the query is split aligned to many target, uses their weighted mean. can help show patterns of more related and distant synteny after WGD)</li>
<li>"mappingQuality" - uses mapping quality from PAF, some adapters don't have this setting</li>
<li>"strand" - colors negative alignments with negColor and positive alignments with posColor</li>
<li>"default" - uses the 'color' config slot</li>
defaultValue: 'default',

slot: thresholdsPalette

thresholdsPalette: {
type: 'stringArray',
defaultValue: ['#094b09', '#2ebd40', '#d5670b', '#ffd84b'],
description: 'threshold colors, used with colorBy:identity',

slot: thresholds

thresholds: {
type: 'stringArray',
defaultValue: ['0.75', '0.5', '0.25', '0'],
description: 'threshold breakpoints, used with colorBy:identity',