BioCircos {BioCircos}R Documentation

BioCircos

Description

Interactive circular visualization of genomic data using ‘htmlwidgets’ and ‘BioCircos.js’

Usage

BioCircos(tracklist = BioCircosTracklist(), genome = "hg19",
  yChr = TRUE, genomeFillColor = "Spectral", chrPad = 0.04,
  displayGenomeBorder = TRUE, genomeBorderColor = "#000",
  genomeBorderSize = 0.5, genomeTicksDisplay = TRUE,
  genomeTicksLen = 5, genomeTicksColor = "#000",
  genomeTicksTextSize = "0.6em", genomeTicksTextColor = "#000",
  genomeTicksScale = 3e+07, genomeLabelDisplay = TRUE,
  genomeLabelTextSize = "10pt", genomeLabelTextColor = "#000",
  genomeLabelDx = 0, genomeLabelDy = 10, genomeLabelOrientation = 0,
  zoom = TRUE, TEXTModuleDragEvent = FALSE,
  SNPMouseOverDisplay = TRUE, SNPMouseOverColor = "#FF0000",
  SNPMouseOverCircleSize = 3, SNPMouseOverCircleOpacity = 0.9,
  SNPMouseOutDisplay = TRUE, SNPMouseOutColor = "none",
  SNPMouseOverTooltipsHtml01 = "Chromosome: ",
  SNPMouseOverTooltipsHtml02 = "<br/>Position: ",
  SNPMouseOverTooltipsHtml03 = "<br/>Value: ",
  SNPMouseOverTooltipsHtml04 = "<br/>",
  SNPMouseOverTooltipsHtml05 = "",
  SNPMouseOverTooltipsBorderWidth = "1px", ARCMouseOverDisplay = TRUE,
  ARCMouseOverColor = "#FF0000", ARCMouseOverArcOpacity = 0.9,
  ARCMouseOutDisplay = TRUE, ARCMouseOutColor = "none",
  ARCMouseOverTooltipsHtml01 = "Chromosome: ",
  ARCMouseOverTooltipsHtml02 = "<br/>Start: ",
  ARCMouseOverTooltipsHtml03 = "<br/>End: ",
  ARCMouseOverTooltipsHtml04 = "<br/>",
  ARCMouseOverTooltipsHtml05 = "",
  ARCMouseOverTooltipsBorderWidth = "1px", LINKMouseOverDisplay = TRUE,
  LINKMouseOverStrokeColor = "#FF00FF", LINKMouseOverOpacity = 0.9,
  LINKMouseOutDisplay = TRUE, LINKMouseOutStrokeColor = "none",
  LINKMouseOverTooltipsHtml01 = "Fusion: ",
  LINKMouseOverTooltipsHtml02 = "",
  LINKMouseOverTooltipsBorderWidth = "1px",
  LINKMouseOverStrokeWidth = 5, LINKMouseOutStrokeWidth = "none",
  BARMouseOutDisplay = TRUE, BARMouseOutColor = "none",
  BARMouseOverDisplay = TRUE, BARMouseOverColor = "#FF0000",
  BARMouseOverOpacity = 0.9,
  BARMouseOverTooltipsHtml01 = "Chromosome: ",
  BARMouseOverTooltipsHtml02 = "<br/>Start: ",
  BARMouseOverTooltipsHtml03 = " End: ",
  BARMouseOverTooltipsHtml04 = "<br/>",
  BARMouseOverTooltipsHtml05 = "<br/>Value: ",
  BARMouseOverTooltipsHtml06 = "",
  BARMouseOverTooltipsBorderWidth = "1px",
  HEATMAPMouseOutDisplay = TRUE, HEATMAPMouseOutColor = "none",
  HEATMAPMouseOverDisplay = TRUE, HEATMAPMouseOverColor = "#FF0000",
  HEATMAPMouseOverOpacity = 0.9,
  HEATMAPMouseOverTooltipsHtml01 = "Chromosome: ",
  HEATMAPMouseOverTooltipsHtml02 = "<br/>Start: ",
  HEATMAPMouseOverTooltipsHtml03 = " End: ",
  HEATMAPMouseOverTooltipsHtml04 = "<br/>",
  HEATMAPMouseOverTooltipsHtml05 = "<br/>Value: ",
  HEATMAPMouseOverTooltipsHtml06 = "",
  HEATMAPMouseOverTooltipsBorderWidth = "1px",
  LINEMouseOutDisplay = TRUE, LINEMouseOutLineOpacity = "none",
  LINEMouseOutLineStrokeColor = "none",
  LINEMouseOutLineStrokeWidth = "none", LINEMouseOverDisplay = T,
  LINEMouseOverLineOpacity = 1,
  LINEMouseOverLineStrokeColor = "#FF0000",
  LINEMouseOverLineStrokeWidth = "none",
  LINEMouseOverTooltipsHtml01 = "Line",
  LINEMouseOverTooltipsBorderWidth = 0, CNVMouseOutDisplay = TRUE,
  CNVMouseOutColor = "none", CNVMouseOutArcOpacity = 1,
  CNVMouseOutArcStrokeColor = "none", CNVMouseOutArcStrokeWidth = 0,
  CNVMouseOverDisplay = TRUE, CNVMouseOverColor = "#FF0000",
  CNVMouseOverArcOpacity = 0.9, CNVMouseOverArcStrokeColor = "#F26223",
  CNVMouseOverArcStrokeWidth = 3,
  CNVMouseOverTooltipsHtml01 = "Chromosome: ",
  CNVMouseOverTooltipsHtml02 = "<br>Start: ",
  CNVMouseOverTooltipsHtml03 = "<br>End: ",
  CNVMouseOverTooltipsHtml04 = "<br>Value: ",
  CNVMouseOverTooltipsHtml05 = "",
  CNVMouseOverTooltipsBorderWidth = "1px", width = NULL,
  height = NULL, elementId = NULL, ...)

Arguments

tracklist

A list of tracks to display.

genome

A list of chromosome lengths to be used as reference for the visualization or 'hg19' to use the chromosomes 1 to 22 and the sexual chromosomes according to the hg19 reference.

yChr

A logical stating if the Y chromosome should be displayed. Used only when genome is set to 'hg19'.

genomeFillColor

The color to display in each chromosome. Can be a RColorBrewer palette name used to generate one color per chromosome, or a character object or vector of character objects stating RGB values in hexadecimal format or base R colors. If the vector is shorter than the reference genome, values will be repeated.

chrPad

Distance between chromosomes.

displayGenomeBorder, genomeBorderColor, genomeBorderSize

Should the reference genome have borders? If yes specify the color, in RGB hexadecimal format, and the thickness.

genomeTicksDisplay, genomeTicksLen, genomeTicksColor, genomeTicksTextSize, genomeTicksTextColor, genomeTicksScale

Should the refence genome have ticks, of which length, color (in hexadecimal RGB format), with labels in which font size and color, and spaced by how many bases?

genomeLabelDisplay, genomeLabelTextSize, genomeLabelTextColor, genomeLabelDx, genomeLabelDy, genomeLabelOrientation

Should the reference genome have labels on each chromosome, in which font size and color? Moreover rotation and radius shifts for the label texts can be added, and the angle between the radius and the label changed.

zoom

Is zooming and moving in the visualization allowed?

TEXTModuleDragEvent

Are text annotations draggable?

SNPMouseOverDisplay

Display the tooltip when mouse hover on a SNP point.

SNPMouseOverColor

Color of the SNP point when hovered by the mouse, in hexadecimal RGB format.

SNPMouseOverCircleSize

Size of the SNP point when hovered by the mouse.

SNPMouseOverCircleOpacity

Opacity of the SNP point when hovered by the mouse.

SNPMouseOutDisplay

Hide tooltip when mouse is not hovering a SNP point anymore.

SNPMouseOutColor

Color of the SNP point when mouse is not hovering a SNP point anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

SNPMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before chromosome number.

SNPMouseOverTooltipsHtml02

Label displayed in tooltip in second position, before genomic position.

SNPMouseOverTooltipsHtml03

Label displayed in tooltip in third position, before value.

SNPMouseOverTooltipsHtml04

Label displayed in tooltip in fourth position, before SNP labels if any.

SNPMouseOverTooltipsHtml05

Label displayed in tooltip in fifth position, after SNP labels if any.

SNPMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

ARCMouseOverDisplay

Display the tooltip when mouse hover on an arc.

ARCMouseOverColor

Color of the arc when hovered by the mouse, in hexadecimal RGB format.

ARCMouseOverArcOpacity

Opacity of the arc when hovered by the mouse.

ARCMouseOutDisplay

Hide tooltip when mouse is not hovering an arc anymore.

ARCMouseOutColor

Color of the arc when mouse is not hovering an arc anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

ARCMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before chromosome number.

ARCMouseOverTooltipsHtml02

Label displayed in tooltip in second position, before genomic position.

ARCMouseOverTooltipsHtml03

Label displayed in tooltip in third position, before value.

ARCMouseOverTooltipsHtml04

Label displayed in tooltip in fourth position, before ARC labels if any.

ARCMouseOverTooltipsHtml05

Label displayed in tooltip in fifth position, after ARC labels if any.

ARCMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

LINKMouseOverDisplay

Display the tooltip when mouse hover on a link.

LINKMouseOverStrokeColor

Color of the link when hovered.

LINKMouseOverOpacity

Opacity of the link when hovered.

LINKMouseOutDisplay

Hide tooltip when mouse is not hovering a link anymore.

LINKMouseOutStrokeColor

Color of the link when mouse is not hovering anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

LINKMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before label.

LINKMouseOverTooltipsHtml02

Label displayed in tooltip in second position, after label.

LINKMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

LINKMouseOverStrokeWidth

Thickness of the link when hovered.

LINKMouseOutStrokeWidth

Thickness of the link when mouse is not hovering a link anymore.

BARMouseOutDisplay

Hide tooltip when mouse is not hovering a bar anymore.

BARMouseOutColor

Color of the bar when mouse is not hovering anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

BARMouseOverDisplay

Display the tooltip when mouse hover on a bar.

BARMouseOverColor

Color of the bar when hovered.

BARMouseOverOpacity

Opacity of the bar when hovered.

BARMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before chromosome number.

BARMouseOverTooltipsHtml02

Label displayed in tooltip in second position, before start position.

BARMouseOverTooltipsHtml03

Label displayed in tooltip in second position, before end position.

BARMouseOverTooltipsHtml04

Label displayed in tooltip in third position, before labels if any.

BARMouseOverTooltipsHtml05

Label displayed in tooltip in fourth position, before values.

BARMouseOverTooltipsHtml06

Label displayed in tooltip in fifth position, after values.

BARMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

HEATMAPMouseOutDisplay

Hide tooltip when mouse is not hovering a box anymore.

HEATMAPMouseOutColor

Color of the box when mouse is not hovering anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

HEATMAPMouseOverDisplay

Display the tooltip when mouse hover on a box.

HEATMAPMouseOverColor

Color of the box when hovered.

HEATMAPMouseOverOpacity

Opacity of the box when hovered.

HEATMAPMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before chromosome number.

HEATMAPMouseOverTooltipsHtml02

Label displayed in tooltip in second position, before start position.

HEATMAPMouseOverTooltipsHtml03

Label displayed in tooltip in second position, before end position.

HEATMAPMouseOverTooltipsHtml04

Label displayed in tooltip in third position, before labels if any.

HEATMAPMouseOverTooltipsHtml05

Label displayed in tooltip in fourth position, before values.

HEATMAPMouseOverTooltipsHtml06

Label displayed in tooltip in fifth position, after values.

HEATMAPMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

LINEMouseOutDisplay

Hide tooltip when mouse is not hovering a line anymore.

LINEMouseOutLineOpacity

Opacity of the line when mouse is not hovering a link anymore.

LINEMouseOutLineStrokeColor

Color of the line when mouse is not hovering anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

LINEMouseOutLineStrokeWidth

Thickness of the line when mouse is not hovering a link anymore.

LINEMouseOverDisplay

Display the tooltip when mouse hover on a line.

LINEMouseOverLineOpacity

Opacity of the line when hovered by the mouse, in hexadecimal RGB format.

LINEMouseOverLineStrokeColor

Color of the line when hovered by the mouse, in hexadecimal RGB format.

LINEMouseOverLineStrokeWidth

Width of the line when hovered by the mouse, in hexadecimal RGB format.

LINEMouseOverTooltipsHtml01

Label displayed in tooltip.

LINEMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

CNVMouseOutDisplay

Hide tooltip when mouse is not hovering an arc anymore.

CNVMouseOutColor

Color of the line when mouse is not hovering anymore, in hexadecimal RGB format. To revert back to original color, use the value "none".

CNVMouseOutArcOpacity

Opacity of the arc when not hovered by the mouse anymore.

CNVMouseOutArcStrokeColor

Color of the arc's stroke when not hovered by the mouse anymore.

CNVMouseOutArcStrokeWidth

Width of the arc's stroke when not hovered by the mouse anymore.

CNVMouseOverDisplay

Display the tooltip when mouse hover on an arc.

CNVMouseOverColor

Color of the arc when hovered by the mouse, in hexadecimal RGB format.

CNVMouseOverArcOpacity

Opacity of the arc when hovered by the mouse.

CNVMouseOverArcStrokeColor

Color of the arc's stroke when hovered by the mouse, in hexadecimal RGB format.

CNVMouseOverArcStrokeWidth

Width of the arc's stroke when hovered by the mouse.

CNVMouseOverTooltipsHtml01

Label displayed in tooltip in first position, before chromosome number.

CNVMouseOverTooltipsHtml02

Label displayed in tooltip in second position, before starting position.

CNVMouseOverTooltipsHtml03

Label displayed in tooltip in second position, before ending position.

CNVMouseOverTooltipsHtml04

Label displayed in tooltip in third position, before value.

CNVMouseOverTooltipsHtml05

Label displayed in tooltip in third position, after value.

CNVMouseOverTooltipsBorderWidth

The thickness of the tooltip borders, with units specified (such as em or px).

width, height

Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.

elementId

the name of the HTML id to be used to contain the visualization.

...

Ignored

Examples

BioCircos(yChr = FALSE, chrPad = 0, genomeFillColor = "Blues")


[Package BioCircos version 0.3.4 Index]