Genome Browser

General parameters used in genome browser


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
Default size in pixels of the coordinates height
Default: 12
Used in: Genome
Flag use to show coordinates
Default: true
Used in: Genome
Default color for the strand direction of the feature in the genome browser
Default: rgb(0,0,0)
Used in: Genome
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
Color for the text of the features in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Size in pixels for the font size of text of the features in the genome browser
Default: 10
Used in: Genome
Font style for the feature name.
Default:
Options: , bold, italic, bold italic
Used in: Genome
Default size in pixels of the quality height
Default: 12
Used in: Genome
Flag use to show quality
Default: true
Used in: Genome
Flag use to show values for the quality
Default: false
Used in: Genome
Default size in pixels of the quality height
Default: 12
Used in: Genome
Flag use to show quality
Default: true
Used in: Genome
Flag use to show values for the quality
Default: false
Used in: Genome
Flag use to stagger the features in the genome panel
Default: false
Used in: Genome
Default size in pixels of the trace height
Default: 40
Used in: Genome
Default triming for nucleotide values in the traces (expressed in percent)
Default: 1
Used in: Genome
Flag use to show traces
Default: true
Used in: Genome
Default size in pixels of the translation height
Default: 12
Used in: Genome
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
genomeResolution option Private
Number to adjust the splines curvature
Default: low
Options: low, medium, high
Used in: Genome
genomeTicks integer
Number of ticks in the genome browser
Default: 50
Used in: Genome
Maximum length in characters a feature label can have so anything above is truncated.
Default: 30
Used in: Genome
Number of ticks to skip between values in the genome browser
Default: 5
Used in: Genome
Color for the adenines and alanines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
Color for the degenerate C/G/T and asparagines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the cytosines and cysteins in the genome browser
Default: rgb(0,0,255)
Used in: Genome
Color for the degenerate A/G/T and aspartic acids in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the glutamic acids in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the end codon in the genome browser
Default: rgb(255,0,0)
Used in: Genome
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
Size in pixels for the font size of text of the sequence in the genome browser
Default: 10
Used in: Genome
Font style for the sequences.
Default:
Options: , bold, italic, bold italic
Used in: Genome
Color for the deletions, insertions and gaps in the genome browser
Default: rgb(255,0,255)
Used in: Genome
Color for the guanines and glycines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the degenerate A/C/T and histidines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
Color for the isoleucines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
Color for the degenerate G/T and lysines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
Color for the leucines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
Color for the degenerate A/G and methionines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
Color for the degenerate A/C/G/T and asparagines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the prolines in the genome browser
Default: rgb(255,165,0)
Used in: Genome
Color for the glutamines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the degenerate A/G and arginines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
Color for the degenerate G/C and serines in the genome browser
Default: rgb(255,165,0)
Used in: Genome
Color for the start codon in the genome browser
Default: rgb(0,204,0)
Used in: Genome
Color for the thymidines and threonines in the genome browser
Default: rgb(255,0,0)
Used in: Genome
Color for the uracils in the genome browser
Default: rgb(255,0,0)
Used in: Genome
Color for the degenerate A/C/G and valines in the genome browser
Default: rgb(0,103,0)
Used in: Genome
Color for the degenerate A/T and tryptophans in the genome browser
Default: rgb(0,0,255)
Used in: Genome
Color for the any aminoacid code in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Color for the degenerate C/T and tyrosines in the genome browser
Default: rgb(0,0,255)
Used in: Genome
Color for the glutamines in the genome browser
Default: rgb(0,0,0)
Used in: Genome
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
Track configurable properties
Default: ['name', 'hideName', 'hideFeatureNames', 'type', 'height', 'fill', 'outline', 'data', 'hide', 'connect', 'subtracksMax', 'highlight']
Used in: Genome
Default color for the strand direction of the tracks in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Default color for the fill of the tracks in the genome browser
Default: rgb(255,255,255)
Used in: Genome
Color for the text of the tracks in the genome browser
Default: rgb(0,0,0)
Used in: Genome
Size in pixels for the font size of text of the tracks in the genome browser
Default: 10
Used in: Genome
Font style for the track name.
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