v0.10.1
Guide
Introduction
Before you start
Design philosophies
Installation and setup
SODA as a TypeScript library
SODA as a JavaScript library
Overview
Annotations
Annotation interfaces
Annotation
PlotAnnotation
SequenceAnnotation
Annotation utilities
Established data formats
Charts
Chart anatomy
Chart configuration
Dimensions configuration
Rendering configuration
Default axes
Row colors
Zooming and panning
Resizing
Zoom and resize callbacks
Chart scales
Chart observers
Rendering
Glyph rendering functions
Glyph selectors
Glyph properties
The canonical rendering pattern
Default rendering routine
RenderParams
Chart.render()
Chart.updateLayout()
Chart.updateRowCount()
Chart.updateDimensions()
Chart.updateDomain()
Chart.draw()
Customizing the rendering routine
Interactivity
Glyph mapping
Api
Classes
AnnotationGroup
Constructors
Properties
end
group
id
start
Methods
add
addAnnotation
Chart
Constructors
Properties
_divHeight
_divMargin
_divOutline
_divOverflowX
_divOverflowY
_divWidth
_padHeight
_padWidth
_renderParams
_transform
_viewportHeight
_viewportWidth
containerSelection
defSelection
divSelection
domainConstraint
draw
glyphModifiers
highlightSelection
id
initialDomain
layout
leftPadSize
lowerPadSize
observers
overflowViewportSelection
padSelection
padSize
postRender
postResize
postZoom
resizable
rightPadSize
rowColors
rowCount
rowHeight
rowOpacity
selector
updateDimensions
updateDomain
updateLayout
updateRowCount
upperPadSize
viewportHeightPx
viewportSelection
viewportWidthPx
xScale
yScale
zoomConstraint
zoomable
Accessors
divHeight
divMargin
divOutline
divOverflowX
divOverflowY
divWidth
domain
range
renderParams
transform
viewportHeight
viewportWidth
Methods
addAxis
addGlyphModifier
addRowStripes
alertObservers
applyGlyphModifiers
calculateContainerDimensions
calculateContainerHeight
calculateContainerWidth
calculateDivDimensions
calculatePadDimensions
calculatePadHeight
calculatePadWidth
calculateViewportDimensions
calculateViewportHeight
calculateViewportWidth
clear
clearHighlight
configureResize
configureZoom
defaultDraw
defaultPostRender
defaultUpdateDimensions
defaultUpdateDomain
defaultUpdateLayout
defaultUpdateRowCount
disableZoom
domainFromMousemoveEvent
domainFromWheelEvent
highlight
initializeXScale
removeRowStripes
render
resetTransform
resize
setDivStyle
setPadAttribute
setViewportAttribute
updateDivHeight
updateDivWidth
updatePadHeight
updateRange
updateViewportHeight
updateViewportPosition
updateViewportProperties
updateViewportWidth
zoom
zoomHighlight
getDomainFromAnnotations
ChartObserver
Constructors
Properties
charts
Methods
add
addChart
alert
RadialChart
Constructors
Properties
_divHeight
_divMargin
_divOutline
_divOverflowX
_divOverflowY
_divWidth
_padHeight
_padWidth
_renderParams
_transform
_viewportHeight
_viewportWidth
axisRadius
containerSelection
defSelection
divSelection
domainConstraint
draw
glyphModifiers
highlightSelection
id
initialDomain
innerRadius
layout
leftPadSize
lowerPadSize
observers
outerRadius
overflowViewportSelection
padSelection
padSize
postRender
postResize
postZoom
resizable
rightPadSize
rowColors
rowCount
rowHeight
rowOpacity
selector
trackHeight
trackOutlineSelection
updateDimensions
updateDomain
updateLayout
updateRowCount
upperPadSize
viewportHeightPx
viewportSelection
viewportWidthPx
xScale
yScale
zoomConstraint
zoomable
Accessors
divHeight
divMargin
divOutline
divOverflowX
divOverflowY
divWidth
domain
range
renderParams
transform
viewportHeight
viewportWidth
Methods
addAxis
addGlyphModifier
addRowStripes
addTrackOutline
alertObservers
applyGlyphModifiers
calculateContainerDimensions
calculateContainerHeight
calculateContainerWidth
calculateDivDimensions
calculatePadDimensions
calculatePadHeight
calculatePadWidth
calculateViewportDimensions
calculateViewportHeight
calculateViewportWidth
clear
clearHighlight
configureResize
configureZoom
defaultDraw
defaultPostRender
defaultUpdateDimensions
defaultUpdateDomain
defaultUpdateLayout
defaultUpdateRowCount
disableZoom
domainFromMousemoveEvent
domainFromWheelEvent
fitRadialDimensions
highlight
initializeXScale
removeRowStripes
render
renderAxis
renderTrackOutline
resetTransform
resize
setDivStyle
setPadAttribute
setViewportAttribute
squareToDivWidth
updateDivHeight
updateDivWidth
updatePadHeight
updateRange
updateViewportHeight
updateViewportPosition
updateViewportProperties
updateViewportWidth
zoom
zoomHighlight
getDomainFromAnnotations
ZoomSyncer
Constructors
Properties
charts
Methods
add
addChart
alert
Interfaces
AggregationConfig
Properties
annotations
criterion
idPrefix
AlignmentAnnotations
Properties
all
gaps
insertions
matches
substitutions
AlignmentConfig
Properties
end
id
query
row
start
target
Annotation
Properties
end
id
start
AnnotationDatum
Properties
a
c
AnnotationGenerationConfig
Properties
generationPattern
maxX
maxY
n
pad
startY
width
AnnotationGroupConfig
Properties
end
group
id
start
ArcConfig
Properties
annotations
chart
fillColor
fillOpacity
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
AreaConfig
Properties
annotations
chart
domain
fillColor
fillDirection
fillOpacity
height
initializeFn
pathData
range
row
rowSpan
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
BarPlotConfig
Properties
annotations
barHeightFn
chart
domain
fillColor
fillOpacity
height
initializeFn
range
row
rowSpan
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
BedAnnotation
Properties
blockCount
blockSizes
blockStarts
chrom
end
id
itemRgb
name
score
start
strand
thickEnd
thickStart
ChartConfig
Properties
axisType
debugShading
divHeight
divMargin
divOutline
divOverflowX
divOverflowY
divWidth
domainConstraint
draw
id
leftPadSize
lowerPadSize
padSize
postRender
postResize
postZoom
resizable
rightPadSize
rowColors
rowCount
rowHeight
rowOpacity
selector
updateDimensions
updateDomain
updateLayout
updateRowCount
upperPadSize
zoomConstraint
zoomable
ChevronGlyphConfig
Properties
annotations
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
ChevronLineConfig
Properties
annotations
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
ChevronRectangleConfig
Properties
annotations
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
ClickConfig
Properties
annotations
chart
click
selector
DynamicTextConfig
Properties
alignmentBaseline
annotations
chart
fillColor
fillOpacity
fontFamily
fontSize
fontStyle
fontWeight
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
text
textAnchor
width
x
y
zoomFn
ExportConfig
Properties
chart
filename
pixelRatio
FullGlyphQueryConfig
Properties
chart
id
selector
Gff3Annotation
Properties
attributes
end
id
phase
score
seqid
source
start
strand
type
GlyphConfig
Properties
annotations
chart
fillColor
fillOpacity
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
GlyphQueryConfig
Properties
chart
id
selector
HighlightConfig
Properties
color
end
opacity
selector
start
HorizontalAxisConfig
Properties
annotations
axisType
chart
domain
fillColor
fillOpacity
fixed
height
initializeFn
range
row
scaleToBinHeight
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
tickSizeOuter
ticks
width
x
y
zoomFn
HoverConfig
Properties
annotations
chart
mouseout
mouseover
selector
LineConfig
Properties
annotations
chart
fillColor
fillOpacity
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
x1
x2
y
y1
y2
zoomFn
LinePlotConfig
Properties
annotations
chart
domain
fillColor
fillOpacity
height
initializeFn
pathData
range
row
rowSpan
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
MapVerticalLayout
Properties
row
rowCount
rowMap
PlotAnnotation
Properties
end
id
start
values
RadialChartConfig
Properties
axisType
debugShading
divHeight
divMargin
divOutline
divOverflowX
divOverflowY
divWidth
domainConstraint
draw
id
leftPadSize
lowerPadSize
padSize
postRender
postResize
postZoom
resizable
rightPadSize
rowColors
rowCount
rowHeight
rowOpacity
selector
trackHeight
updateDimensions
updateDomain
updateLayout
updateRowCount
upperPadSize
zoomConstraint
zoomable
RectangleConfig
Properties
annotations
chart
fillColor
fillOpacity
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
RenderParams
Properties
annotations
end
rowCount
start
SequenceAnnotation
Properties
end
id
sequence
start
SequenceConfig
Properties
annotations
chart
fillColor
fillOpacity
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
width
x
y
zoomFn
SimpleTextConfig
Properties
alignmentBaseline
annotations
chart
fillColor
fillOpacity
fontFamily
fontSize
fontStyle
fontWeight
height
initializeFn
row
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
text
textAnchor
width
x
y
zoomFn
TooltipConfig
Properties
annotations
backgroundColor
borderRadius
chart
opacity
padding
selector
text
textColor
VerticalAxisConfig
Properties
annotations
axisType
chart
domain
fillColor
fillOpacity
height
initializeFn
range
row
rowSpan
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
target
tickSizeOuter
ticks
width
x
y
zoomFn
VerticalLayout
Properties
row
rowCount
Functions
aggregateIntransitive
aggregateTransitive
arc
area
axisRadialInner
axisRadialOuter
barPlot
chevronLine
chevronRectangle
clickBehavior
dynamicText
exportPng
generateAnnotations
generateId
generatePlotAnnotations
generateSequenceAnnotations
getAlignmentAnnotations
getAllAnnotationIds
getAnnotationById
getAxis
greedyGraphLayout
heatmap
heuristicGraphLayout
horizontalAxis
hoverBehavior
intervalGraphLayout
keyFromQueryConfig
line
linePlot
parseBedRecords
parseGff3Records
parseOrientation
queryGlyphMap
radialRectangle
rectangle
removeGlyphsByQuery
resolveValue
sequence
setKeySeparator
simpleText
slicePlotAnnotation
sliceSequenceAnnotation
tooltip
unmapAnnotationById
verticalAxis
Enumerations
AxisType
Members
Bottom
Left
Right
Top
BindTarget
Members
Defs
Overflow
Viewport
FillDirection
Members
Down
Up
GenerationPattern
Members
Random
Sequential
Orientation
Members
Forward
Reverse
Unknown
Unoriented
SODA GitHub
SODA issues
SODA website
SODA
»
Api
»
Interfaces
»
SequenceAnnotation
SequenceAnnotation
interface
SequenceAnnotation
Properties
end
end
:
number
id
id
:
string
sequence
sequence
:
string
start
start
:
number
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v: v0.10.1
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