Ideograms : General parameters for Ideograms

# ideogram

Ideogram. Additional ideograms can be loaded by appending to the CanvasXpress.chromosomes object. The format of the ideogram is based on the R data for USCS.hg19.chr
CanvasXpress.chromosomes = {
  hg19 : {
    order : [ 1, 2, 3, 4, 5, 6, 7, 8, ...],
    data : {
      1 : [ [ 0, 2300000, "p36.33", "gneg" ], ...],
      2 : [ [ 0, 4300000, "p25.3", "gneg" ], ...],
    }
  }
}

Type: string

Default: hg38

Options: hg38

Used in: Circular, Genome

# ideogramChromosome

Factor name included in the data.z object used to map to the chromosome number

Type: string

Default: chr

Used in: Circular, Genome

# ideogramChromosomeNumber

Chromosome number

Type: string

Default: 1

Used in: Circular, Genome

# ideogramChromosomePosition

Factor name included in the data.z object used to map to the chromosome position

Type: string

Default: pos

Used in: Circular, Genome

# ideogramHeight

Default size in pixels of the ideogram height

Type: integer

Default: 20

Used in: Circular, Genome

# ideogramSegmentAlign

Alignment (or position) for the ideogram segment

Type: string

Default: center

Options: left, center, right

Used in: Circular, Genome

# ideogramSegmentBaseline

Baseline (or reference line) for the ideogram segment

Type: string

Default: middle

Options: top, middle, bottom

Used in: Circular, Genome

# ideogramSegmentColor

Color for the text in ideogram segment

Type: color

Default: rgb(0,0,0)

Used in: Circular, Genome

# ideogramSegmentFontSize

Font size for the text in ideogram segment. Be aware that auto scaling font must be turned off for this property to take effect. A more convenient way to modify the size is to use the ideogramSegmentScaleFontFactor

Type: integer

Default: 10

Used in: Circular, Genome

# ideogramSegmentFontStyle

Font style for the ideogram segment

Type: string

Default:

Options: , bold, italic, bold italic

Used in: Circular, Genome

# ideogramSegmentMargin

Margin to pad or separate the characters in the ideogram segment

Type: float

Default: 8

Used in: Circular, Genome

# ideogramSegmentRotate

Rotation in degrees for the ideogram segment

Type: integer

Default:

Used in: Circular, Genome

# ideogramSegmentScaleFontFactor

Scaling factor used to increase or decrease the ideogram segment font size in the canvas

Type: float

Default: 1

Used in: Circular, Genome

# ideogramShowFullChromosome

Flag to show the full chromosome

Type: boolean

Default: true

Used in: Circular, Genome

# showIdeogram

Flag to show/hide the Human Chromosome Ideogram. Force circular plots to be two dimensional

Type: boolean

Default: false

Used in: Circular, Genome