| 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 |
elementId |
the name of the HTML id to be used to contain the visualization. |
... |
Ignored |
Examples
BioCircos(yChr = FALSE, chrPad = 0, genomeFillColor = "Blues")