Genome Browser

General parameters used in genome browser

featureConfigurableProperties array
Feature configurable properties
Default: ['id', 'name', 'label', 'hideName', 'fill', 'outline', 'dir', 'showDir', 'connect', 'offset', 'data', 'subtype', 'quality', 'signalToNoise', 'coordinate', 'sequence', 'trace', 'gaps', 'translate', 'hide', 'counter']
Used in: Genome
featureCoordinateHeight integer
Default size in pixels of the coordinates height
Default: 12
Used in: Genome
featureCoordinateShow boolean
Flag use to show coordinates
Default: true
Used in: Genome
featureDirColor color
Default color for the strand direction of the feature in the genome browser
Default: rgb(0,0,0)
Used in: Genome
featureFillColor color
Default color for the fill of the feature in the genome browser
Default: rgb(255,255,255)
Used in: Genome
featureHeightDefault integer
Default size in pixels of the feature height
Default: 14
Used in: Genome
featureNameFont font Private
Font for the text of the features in the genome browser
Default:
Used in: Genome
featureNameFontColor color
Color for the text of the features in the genome browser
Default: rgb(0,0,0)
Used in: Genome
featureNameFontSize integer
Size in pixels for the font size of text of the features in the genome browser
Default: 10
Used in: Genome
featureNameFontStyle option
Font style for the feature name. @default
Default:
Options: , bold, italic, bold italic
Used in: Genome
featureQualityHeight integer
Default size in pixels of the quality height
Default: 12
Used in: Genome
featureQualityShow boolean
Flag use to show quality
Default: true
Used in: Genome
featureQualityValues boolean
Flag use to show values for the quality
Default: false
Used in: Genome
featureSignalToNoiseHeight integer
Default size in pixels of the quality height
Default: 12
Used in: Genome
featureSignalToNoiseShow boolean
Flag use to show quality
Default: true
Used in: Genome
featureSignalToNoiseValues boolean
Flag use to show values for the quality
Default: false
Used in: Genome
featureStaggered boolean
Flag use to stagger the features in the genome panel
Default: false
Used in: Genome
featureTraceHeight integer
Default size in pixels of the trace height
Default: 40
Used in: Genome
featureTraceTrim integer
Default triming for nucleotide values in the traces (expressed in percent)
Default: 1
Used in: Genome
featureTracesShow boolean
Flag use to show traces
Default: true
Used in: Genome
featureTranslateHeight integer
Default size in pixels of the translation height
Default: 12
Used in: Genome
featureTranslateShow boolean
Flag use to show tranlation
Default: true
Used in: Genome
featureTypeDefault option
Default type for the feature in the genome browser
Default: line
Options: box, bar, heatmap, sequence, triangle, line
Used in: Genome
featureWidthDefault integer
Default size in pixels of the feature width
Default: 3
Used in: Genome
filterFeatureBy filter
Filter features by their properties used in genome browser *
Default: []
Used in: Genome
genomeResolution option Private
Number to adjust the splines curvature
Default:
Options: low, medium, high
Used in: Genome
genomeTicks integer
Number of ticks in the genome browser
Default: 50
Used in: Genome
maxFeatureStringLen integer
Maximum length in characters a feature label can have so anything above is truncated.
Default: 50
Used in: Genome
periodTicksLabels integer
Number of ticks to skip between values in the genome browser
Default: 5
Used in: Genome
sequenceAColor color
Color for the adenines and alanines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
sequenceBColor color
Color for the degenerate C/G/T and asparagines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceCColor color
Color for the cytosines and cysteins in the genome browser
Default: rgb(0,0,255)
Used in: Genome
sequenceDColor color
Color for the degenerate A/G/T and aspartic acids in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceEColor color
Color for the glutamic acids in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceEndColor color
Color for the end codon in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceFColor color
Color for the phenylalanines in the genome browser
Default: rgb(0,0,255)
Used in: Genome
sequenceFill color
Color for the background when showing sequnces in the box or sequence object in the Genome. The default is to use the background of the object. If specied a valid color then all the background of sequences will be uniform
Default: false
Used in: Genome
sequenceFont font Private
Font for the text of the sequence in the genome browser
Default:
Used in: Genome
sequenceFontSize integer
Size in pixels for the font size of text of the sequence in the genome browser
Default: 10
Used in: Genome
sequenceFontStyle option
Font style for the sequences. @default
Default:
Options: , bold, italic, bold italic
Used in: Genome
sequenceGAPColor color
Color for the deletions, insertions and gaps in the genome browser
Default: rgb(255,0,255)
Used in: Genome
sequenceGColor color
Color for the guanines and glycines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceHColor color
Color for the degenerate A/C/T and histidines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceIColor color
Color for the isoleucines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
sequenceKColor color
Color for the degenerate G/T and lysines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceLColor color
Color for the leucines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
sequenceMColor color
Color for the degenerate A/G and methionines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
sequenceNColor color
Color for the degenerate A/C/G/T and asparagines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequencePColor color
Color for the prolines in the genome browser
Default: rgb(255,165,0)
Used in: Genome
sequenceQColor color
Color for the glutamines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceRColor color
Color for the degenerate A/G and arginines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceSColor color
Color for the degenerate G/C and serines in the genome browser
Default: rgb(255,165,0)
Used in: Genome
sequenceStartColor color
Color for the start codon in the genome browser
Default: rgb(0,204,0)
Used in: Genome
sequenceTColor color
Color for the thymidines and threonines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceUColor color
Color for the uracils in the genome browser
Default: rgb(255,0,0)
Used in: Genome
sequenceVColor color
Color for the degenerate A/C/G and valines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
sequenceWColor color
Color for the degenerate A/T and tryptophans in the genome browser
Default: rgb(0,0,255)
Used in: Genome
sequenceXColor color
Color for the any aminoacid code in the genome browser
Default: rgb(0,0,0)
Used in: Genome
sequenceYColor color
Color for the degenerate C/T and tyrosines in the genome browser
Default: rgb(0,0,255)
Used in: Genome
sequenceZColor color
Color for the glutamines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
showFeatureNameThereshold integer
Threshehold used to set te limit when there are too many features in the genome browser
Default: 20
Used in: Genome
subtracksMaxDefault integer
Maximum number of subtracks to show in a track
Default: 8
Used in: Genome
trackConfigurableProperties array
Track configurable properties
Default: ['name', 'hideName', 'hideFeatureNames', 'type', 'height', 'fill', 'outline', 'data', 'hide', 'connect', 'subtracksMax', 'highlight']
Used in: Genome
trackDirColor color
Default color for the strand direction of the tracks in the genome browser
Default: rgb(0,0,0)
Used in: Genome
trackFillColor color
Default color for the fill of the tracks in the genome browser
Default: rgb(255,255,255)
Used in: Genome
trackNameFont font Private
Font for the text of the tracks in the genome browser
Default:
Used in: Genome
trackNameFontColor color
Color for the text of the tracks in the genome browser
Default: rgb(0,0,0)
Used in: Genome
trackNameFontSize integer
Size in pixels for the font size of text of the tracks in the genome browser
Default: 10
Used in: Genome
trackNameFontStyle option
Font style for the track name. @default
Default:
Options: , bold, italic, bold italic
Used in: Genome
wireColor color
Color for the ticks in the genome browser
Default: rgba(204,204,204,0.1)
Used in: Genome
 
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