Help for package BioCircos

Title:

Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'

Version:

0.3.4

Description:

Implement in 'R' interactive Circos-like visualizations of genomic data, to map information such as genetic variants, genomic fusions and aberrations to a circular genome, as proposed by the 'JavaScript' library 'BioCircos.js', based on the 'JQuery' and 'D3' technologies. The output is by default displayed in stand-alone HTML documents or in the 'RStudio' viewer pane. Moreover it can be integrated in 'R Markdown' documents and 'Shiny' applications.

Depends:

R (≥ 3.1.0)

License:

GPL-2 | file LICENSE

Encoding:

UTF-8

URL:

https://github.com/lvulliard/BioCircos.R

LazyData:

true

RoxygenNote:

6.1.1

Suggests:

knitr, rmarkdown

VignetteBuilder:

knitr

Imports:

RColorBrewer, htmlwidgets, jsonlite, plyr, grDevices

NeedsCompilation:

Packaged:

2019-03-12 15:03:38 UTC; lvulliard

Author:

Loan Vulliard [trl, cre], Xiaowei Chen [aut], Ya Cui [aut]

Maintainer:

Loan Vulliard <lvulliard@cemm.at>

Repository:

CRAN

Date/Publication:

2019-03-19 16:23:26 UTC

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")

Shiny bindings for BioCircos

Description

Output and render functions for using BioCircos within Shiny applications and interactive Rmd documents.

Usage

BioCircosOutput(outputId, width = "100%", height = "400px")

renderBioCircos(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId

output variable to read from

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.

expr

An expression that generates a BioCircos

env

The environment in which to evaluate expr.

quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Create a track with arcs to be added to a BioCircos tracklist

Description

Arcs are defined by beginning and ending genomic coordinates

Usage

BioCircosArcTrack(trackname, chromosomes, starts, ends,
  colors = "#40B9D4", labels = "", opacities = 1, maxRadius = 0.9,
  minRadius = 0.5, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each arc is found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

starts, ends

Vectors containing the coordinates on which each arc begins or ends. Values should be inferior to the chromosome lengths given in the genome parameter of the BioCircos function.

colors

The colors for each arc. Can be a RColorBrewer palette name used to generate one color per arc, 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 number of arcs, values will be repeated.

labels

One or multiple character objects to label each arc.

opacities

One or multiple opacity values for the arcs, between 0 and 1.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

...

Ignored

Examples

BioCircos(BioCircosArcTrack('ArcTrack', chromosomes = 1:5, starts = 2e+7*1:5, ends = 2.5e+7*2:6))

Create a background track to be added to a BioCircos tracklist

Description

Simple background to display behind another track

Usage

BioCircosBackgroundTrack(trackname, fillColors = "#EEEEFF",
  borderColors = "#000000", maxRadius = 0.9, minRadius = 0.5,
  borderSize = 0.3, ...)

Arguments

trackname

The name of the new track.

fillColors

The color of the background element, in hexadecimal RGB format.

borderColors

The color of the background borders, in hexadecimal RGB format.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

borderSize

The thickness of the background borders.

...

Ignored

Examples

BioCircos(BioCircosBackgroundTrack('bgTrack', fillColors="#FFEEEE", borderSize = 1))

Create a track with a bar plot to be added to a BioCircos tracklist

Description

Bins are defined by a genomic range and associated with a numerical value

Usage

BioCircosBarTrack(trackname, chromosomes, starts, ends, values,
  labels = "", maxRadius = 0.9, minRadius = 0.5, color = "#40B9D4",
  range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each bar is found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

starts, ends

Vectors containing the coordinates on which each bin begins or ends.

values

A vector of numerical values associated with each bin, used to determine the height of each bar on the track.

labels

One or multiple character objects to label each bar.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

color

The color for the bars, in hexadecimal RGB format.

range

Vector of values to be mapped to the minimum and maximum radii of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

BioCircos(BioCircosBarTrack('BarTrack', chromosomes = 1:3, starts = 1e+7*2:4, ends = 2.5e+7*2:4, 
  values = 1:3, labels = c('A ', 'B ', 'C '), range = c(0,4)) + BioCircosBackgroundTrack('BGTrack'))

Create a track with concentric arcs to be added to a BioCircos tracklist

Description

Arcs are defined by a genomic range and radially associated with a numerical value

Usage

BioCircosCNVTrack(trackname, chromosomes, starts, ends, values,
  maxRadius = 0.9, minRadius = 0.5, width = 1, color = "#40B9D4",
  range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each arc is found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

starts, ends

Vectors containing the coordinates on which each arc begins or ends.

values

A vector of numerical values associated with each bin, used to determine the height of each bar on the track.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

width

The thickness of the arc

color

The color for the arcs, in hexadecimal RGB format.

range

Vector of values to be mapped to the minimum and maximum radii of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

BioCircos(BioCircosCNVTrack('BarTrack', chromosomes = 1:3, starts = 1e+7*2:4, ends = 2.5e+7*2:4, 
  values = 1:3, color = "#BB0000", maxRadius = 0.85, minRadius = 0.55) 
  + BioCircosBackgroundTrack('BGTrack'))

Create a heatmap track to be added to a BioCircos tracklist

Description

Heatmaps are defined by the genomic range and the color-associated numerical value of each box of the heatmap layer

Usage

BioCircosHeatmapTrack(trackname, chromosomes, starts, ends, values,
  labels = "", maxRadius = 0.9, minRadius = 0.5,
  color = c("#40B9D4", "#F8B100"), range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each box is found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

starts, ends

Vectors containing the coordinates on which each box begins or ends.

values

A vector of numerical values associated with each box, used to determine the height of each bar on the track.

labels

One or multiple character objects to label each bar.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

color

a vector of the colors in hexadecimal RGB format to be mapped to the minimum and maximum values of the track. Colors of intermediate values will be linearly interpolated between this two colors.

range

a vector of the values to be mapped to the minimum and maximum colors of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

BioCircos(BioCircosHeatmapTrack('HmTrack', chromosomes = 1:3, starts = 1e+7*2:4, ends = 2.5e+7*2:4, 
  values = 1:3, labels = c('A ', 'B ', 'C ')))

Create a track with lines to be added to a BioCircos tracklist

Description

Lines are defined by genomic coordinates and values of an ordered set of points, that will define the edges of the segments.

Usage

BioCircosLineTrack(trackname, chromosomes, positions, values,
  color = "#40B9D4", width = 2, maxRadius = 0.9, minRadius = 0.5,
  range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each vertex is found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

positions

A vector containing the coordinates on which each vertex are found. Values should be inferior to the chromosome lengths given in the genome parameter of the BioCircos function.

values

A vector of numerical values associated with each vertex, used to determine the radial coordinate of each vertex on the visualization.

color

The color of the line in hexadecimal RGB format.

width

The line width.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

range

Vector of values to be mapped to the minimum and maximum radii of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

BioCircos(BioCircosLineTrack('LnId', rep(1,30), 2e+6*(1:100), log(1:100)) 
  + BioCircosBackgroundTrack('BGId'))

Create an inner track with links to be added to a BioCircos tracklist

Description

Links are defined by beginning and ending genomic coordinates of the 2 regions to linked, such as the positions linked in genomic fusions.

Usage

BioCircosLinkTrack(trackname, gene1Chromosomes, gene1Starts, gene1Ends,
  gene2Chromosomes, gene2Starts, gene2Ends, color = "#40B9D4",
  labels = "", maxRadius = 0.4, width = "0.1em", gene1Names = "",
  gene2Names = "", displayAxis = TRUE, axisColor = "#B8B8B8",
  axisWidth = 0.5, axisPadding = 0, displayLabel = TRUE,
  labelColor = "#000000", labelSize = "1em", labelPadding = 3, ...)

Arguments

trackname

The name of the new track.

gene1Chromosomes, gene1Starts, gene1Ends, gene1Names, gene2Chromosomes, gene2Starts, gene2Ends, gene2Names

Vectors with the chromosomes, genomic coordinates of beginning and end, and names of both genes to link. Chromosomes and positions should respect the chromosome names and lengths given in the genome parameter of the BioCircos function.

color

The color for the links, in hexadecimal RGB format.

labels

A vector of character objects to label each link.

maxRadius

Where the track should end, in proportion of the inner radius of the plot.

width

The thickness of the links.

displayAxis

Display additional axis (i.e. circle) around the track.

axisColor, axisWidth, axisPadding

Color, thickness and padding of the additional axis.

displayLabel

Display labels of the track.

labelColor, labelSize, labelPadding

Color, font size and padding of the labels around the track.

...

Ignored

Examples

start_chromosomes <- 1:5
end_chromosomes <- 2*10:6
start_pos <- 2.5e+7*2:6
end_pos <- 2e+7*1:5
BioCircos(BioCircosLinkTrack('LinkTrack', start_chromosomes, start_pos, start_pos+1,
  end_chromosomes, end_pos, end_pos+1, color = '#FF00FF'))

Create a track with SNPs to be added to a BioCircos tracklist

Description

SNPs are defined by genomic coordinates and associated with a numerical value

Usage

BioCircosSNPTrack(trackname, chromosomes, positions, values,
  colors = "#40B9D4", labels = "", size = 2, shape = "circle",
  opacities = 1, maxRadius = 0.9, minRadius = 0.5, range = 0, ...)

Arguments

trackname

The name of the new track.

chromosomes

A vector containing the chromosomes on which each SNP are found. Values should match the chromosome names given in the genome parameter of the BioCircos function.

positions

A vector containing the coordinates on which each SNP are found. Values should be inferior to the chromosome lengths given in the genome parameter of the BioCircos function.

values

A vector of numerical values associated with each SNPs, used to determine the radial coordinates of each point on the visualization.

colors

The colors for each point. Can be a RColorBrewer palette name used to generate one color per point, 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 number of points, values will be repeated.

labels

One or multiple character objects to label each point.

size

The size of each point.

shape

Shape of the points. Can be "circle" or "rect".

opacities

One or multiple opacity values for the points, between 0 and 1.

minRadius, maxRadius

Where the track should begin and end, in proportion of the inner radius of the plot.

range

Vector of values to be mapped to the minimum and maximum radii of the track. Default to 0, mapping the minimal and maximal values input in the values parameter.

...

Ignored

Examples

BioCircos(BioCircosSNPTrack('SNPTrack', chromosomes = 1:3, positions = 1e+7*2:4, 
  values = 1:3, colors = "Accent", labels = c('A', 'B', 'C')) + BioCircosBackgroundTrack('BGTrack'))

Create a Text track to be added to a BioCircos tracklist

Description

Simple text annotation displayed in the visualization

Usage

BioCircosTextTrack(trackname, text, x = -0.15, y = 0, size = "1.2em",
  weight = "bold", opacity = 1, color = "#000000", ...)

Arguments

trackname

The name of the new track.

text

The text to be displayed.

x, y

Coordinates of the lower left corner of the annotation, in proportion of the inner radius of the plot.

size

Font size, with units specified (such as em or px).

weight

Font weight. Can be "normal", "bold", "bolder" or "lighter".

opacity

Font opacity.

color

Font color, in hexadecimal RGB format.

...

Ignored

Examples

BioCircos(BioCircosTextTrack('textTrack', 'Annotation', color = '#DD2222', x = -0.3))

Create a list of BioCircos tracks

Description

This allows the use of the '+' and '-' operator on these lists

Usage

BioCircosTracklist()

## S3 method for class 'BioCircosTracklist'
x + ...

## S3 method for class 'BioCircosTracklist'
x - ...

Arguments

x

The tracklist on which other tracks should be added or removed.

...

The tracks to add (as tracklists) or to remove (as track names).