v0.7.0
Introduction
Before you start
Design philosophies
Installation and setup
SODA as a TypeScript library
SODA as a JavaScript library
Tutorial
The basics
Creating a Chart
Rendering Annotations
Adding an axis
Changing the row height
Changing the pad size
Enabling zooming
Constraining the zoom level
Enabling resizing
Enabling row stripes
Setting an explicit render range
Custom rendering
Overriding the default Chart rendering routine - colored rectangles
Coloring rectangles using callbacks
Lines
Arcs
Chevron lines
Chevron rectangles
Text
Vertical layout
Automatic layout
Explicitly calling a SODA layout function
Comparing SODA layout functions
Interval layout
Greedy layout
Heuristic layout
Externally defining a layout
Using common Bioinformatics data formats
Rendering BED data
Rendering GFF3 data
Interactivity
Click behaviors
Hover behaviors
Tooltips
Exporting images
Multi-chart visualizations
Multiple charts rendering the same Annotations
Syncing the zoom level across multiple charts
API
Classes
Annotation
Constructors
Properties
end
id
row
start
suppressWarnings
width
Accessors
w
x
x2
y
AnnotationGroup
Constructors
Properties
end
group
id
row
start
suppressWarnings
width
Accessors
w
x
x2
y
Methods
add
Bed12Annotation
Constructors
Properties
blockCount
blockSizes
blockStarts
chrom
end
id
itemRgb
name
row
score
start
strand
suppressWarnings
thickEnd
thickStart
width
Accessors
w
x
x2
y
Bed3Annotation
Constructors
Properties
chrom
end
id
row
start
suppressWarnings
width
Accessors
w
x
x2
y
Bed6Annotation
Constructors
Properties
chrom
end
id
name
row
score
start
strand
suppressWarnings
width
Accessors
w
x
x2
y
Bed9Annotation
Constructors
Properties
chrom
end
id
itemRgb
name
row
score
start
strand
suppressWarnings
thickEnd
thickStart
width
Accessors
w
x
x2
y
BedAnnotation
Constructors
Properties
blockCount
blockSizes
blockStarts
chrom
end
id
itemRgb
name
row
score
start
strand
suppressWarnings
thickEnd
thickStart
width
Accessors
w
x
x2
y
Chart
Constructors
Properties
_axisAnn
_containerSelection
_padHeight
_padWidth
_renderEnd
_renderParams
_renderStart
_rowStripePatternSelection
_rowStripeRectSelection
_selector
_transform
_viewportHeight
_viewportWidth
axis
defSelection
glyphModifiers
id
inRender
observers
overflowViewportSelection
padSelection
padSize
postRender
preRender
resizable
rowCount
rowHeight
rowStripes
scaleExtent
translateExtent
viewportSelection
xScale
xScaleBase
zoomable
Accessors
containerSelection
padHeight
padWidth
renderEnd
renderParams
renderStart
rowStripePatternSelection
rowStripeRectSelection
selector
transform
viewportHeight
viewportWidth
Methods
addAxis
addGlyphModifier
alertObservers
applyGlyphModifiers
applyLayoutAndSetRowCount
calculateContainerDimensions
calculatePadDimensions
calculatePadHeight
calculatePadWidth
calculateViewportDimensions
calculateViewportHeight
calculateViewportWidth
configureResize
configureZoom
disableZoom
fitPadHeight
fitRowStripes
fitViewport
getContainerHeight
getContainerWidth
getSemanticViewRange
initializeXScale
initializeXScaleFromRenderParams
render
rescaleXScale
resetTransform
resize
setRowStripes
setToContainerDimensions
squareToContainerHeight
squareToContainerWidth
zoom
inferRenderRange
ChartObserver
Constructors
Properties
charts
Methods
add
addChart
alert
Gff3Annotation
Constructors
Properties
attributes
end
id
phase
row
score
seqid
source
start
strand
suppressWarnings
type
width
Accessors
w
x
x2
y
PlotAnnotation
Constructors
Properties
end
id
maxValue
minValue
pointWidth
points
row
start
suppressWarnings
width
Accessors
w
x
x2
y
SequenceAnnotation
Constructors
Properties
characters
columnTypes
end
id
row
sequence
start
suppressWarnings
width
Accessors
w
x
x2
y
ZoomSyncer
Constructors
Properties
charts
Methods
add
addChart
alert
Interfaces
AggregationConfig
Properties
annotations
criterion
idPrefix
AnnotationConfig
Properties
end
id
row
start
suppressWarnings
width
AnnotationConfigWithGroup
Properties
end
group
id
row
start
suppressWarnings
width
AnnotationDatum
Properties
a
c
AnnotationGenerationConfig
Properties
generationPattern
maxX
maxY
n
pad
startY
width
ArcConfig
Properties
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
BarPlotConfig
Properties
annotations
barHeightFn
binSpan
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
ChartConfig
Properties
axis
height
id
inRender
padSize
postRender
preRender
resizable
rowCount
rowHeight
rowStripes
scaleExtent
selector
translateExtent
width
zoomable
ChevronGlyphConfig
Properties
annotations
bindTarget
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
ChevronLineConfig
Properties
annotations
bindTarget
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
ChevronRectangleConfig
Properties
annotations
bindTarget
chart
chevronFillColor
chevronFillOpacity
chevronHeight
chevronSpacing
chevronStrokeColor
chevronStrokeOpacity
chevronWidth
fillColor
fillOpacity
height
initializeFn
orientation
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
ClickConfig
Properties
annotations
chart
click
ExportConfig
Properties
chart
filename
pixelRatio
Gff3AnnotationConfig
Properties
attributes
end
id
phase
row
score
seqid
source
start
strand
suppressWarnings
type
width
Gff3Record
Properties
attributes
phase
score
seqid
source
strand
type
GlyphConfig
Properties
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
GlyphMapping
Properties
chart
selection
HorizontalAxisConfig
Properties
annotations
axisType
bindTarget
chart
domain
fillColor
fillOpacity
fixed
height
initializeFn
range
scaleToBinHeight
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
tickSizeOuter
ticks
width
x
y
zoomFn
HoverConfig
Properties
annotations
chart
mouseout
mouseover
LineConfig
Properties
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
x1
x2
y
y1
y2
zoomFn
LinePlotConfig
Properties
annotations
binSpan
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
pathData
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
PlotAnnotationConfig
Properties
end
id
row
start
suppressWarnings
width
xValues
yValues
RectangleConfig
Properties
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
RenderParams
Properties
annotations
autoLayout
end
initializeXScale
layoutFn
rowCount
start
SequenceAnnotationConfig
Properties
columnTypes
end
id
row
sequence
start
suppressWarnings
width
SequenceConfig
Properties
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
width
x
y
zoomFn
TextConfig
Properties
alignmentBaseline
annotations
bindTarget
chart
fillColor
fillOpacity
height
initializeFn
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
textAnchor
textFn
width
x
y
zoomFn
TooltipConfig
Properties
annotations
backgroundColor
borderRadius
chart
opacity
padding
text
textColor
Transform
Properties
k
x
y
VerticalAxisConfig
Properties
annotations
axisType
binSpan
bindTarget
chart
domain
fillColor
fillOpacity
fixed
height
initializeFn
range
selector
strokeColor
strokeDashArray
strokeDashOffset
strokeLineCap
strokeLineJoin
strokeOpacity
strokeWidth
tickSizeOuter
ticks
width
x
y
zoomFn
ViewRange
Properties
end
start
width
Functions
aggregateIntransitive
aggregateTransitive
arc
barPlot
chevronLine
chevronRectangle
clickBehavior
exportPng
generateAnnotations
generateId
generatePlotAnnotations
generateSequenceAnnotations
getAllAnnotationIds
getAnnotationById
getAxis
getHorizontalAxisAnnotation
greedyGraphLayout
heatmap
heuristicGraphLayout
horizontalAxis
hoverBehavior
intervalGraphLayout
line
linePlot
parseBed12Record
parseBed3Record
parseBed6Record
parseBed9Record
parseBedRecord
parseGff3Record
parseOrientation
parseRecordsFromString
queryGlyphMap
rectangle
resolveValue
sequence
text
tooltip
verticalAxis
Enumerations
AxisType
Members
Bottom
Left
Right
Top
BindTarget
Members
Defs
Overflow
Viewport
ColumnType
Members
Deletion
Insertion
Match
Substitution
GenerationPattern
Members
Random
Sequential
Orientation
Members
Forward
Reverse
Unknown
Unoriented
Type aliases
AnnotationGroupConfig
Bed12AnnotationConfig
Bed3AnnotationConfig
Bed6AnnotationConfig
Bed9AnnotationConfig
BedAnnotationConfig
GlyphCallback
GlyphProperty
SODA GitHub
SODA issues
SODA website
SODA
»
API
»
Enumerations
Enumerations
AxisType
Members
BindTarget
Members
ColumnType
Members
GenerationPattern
Members
Orientation
Members
Read the Docs
v: v0.7.0
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