Package 'interacCircos'

Title: The Generation of Interactive Circos Plot
Description: Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. 'interacCircos' are inspired by 'circosJS', 'BioCircos.js' and 'NG-Circos' and we integrate the modules of 'circosJS', 'BioCircos.js' and 'NG-Circos' into this R package, based on 'htmlwidgets' framework.
Authors: Zhe Cui [aut, cre]
Maintainer: Zhe Cui <[email protected]>
License: GPL-3
Version: 1.17.0
Built: 2024-10-30 08:32:45 UTC
Source: https://github.com/bioc/interacCircos

Help Index

Arc plot example data

Description

The data is in matrix with column names

Usage

arcExample

Format

A data frame with 7 columns:

chr

chromosome

start

start position

end

end position

color

color

des

description

link

hyperlink

html

The external html language

Bubble plot example data

Description

The data is in matrix with column names

Usage

bubbleExample

Format

A data frame with 8 columns:

chr

chromosome

start

start position

end

end position

name

name for description

value

value

color

specified color for bubble

layer

layer number

html

The external html language

Example data of chord plot of circosJS

Description

The data is in matrix with column names

Usage

chord.pExample

Format

A data frame in which each row represents the relationship from one genome position(source) to another one(target):

source_chr

chromosome name of source

source_start

start position of source

source_end

end position of source

target_chr

chromosome name of target

target_start

start position of target

target_end

end position of target

Example data of chord plot of NG-Circos

Description

The data is in matrix with column names. The order and number is same as column, representing the same items

Usage

chordExample

Format

A data frame in which each value represents the relationship from a column to a row:

C.CK

Genome 1, the name for each arc

C.NPK

Genome 2, the name for each arc

GC.CK

Genome 2, the name for each arc

GC.NPK

Genome 2, the name for each arc

Alphaproteobacteria

Genome 2, the name for each arc

Betaproteobacteria

Genome 2, the name for each arc

Gammaproteobacteria

Genome 2, the name for each arc

Deltaproteobacteria

Genome 8, the name for each arc

Acidobacteria

Genome 9, the name for each arc

Actinobacteria

Genome 10, the name for each arc

Bacteroidetes

Genome 11, the name for each arc

Chloroflexi

Genome 12, the name for each arc

Firmicutes

Genome 13, the name for each arc

Gemmatimonadetes

Genome 14, the name for each arc

Planctomycetes

Genome 15, the name for each arc

Thaumarchaeota

Genome 16, the name for each arc

Verrucomicrobia

Genome 17, the name for each arc

Ascomycota

Genome 18, the name for each arc

Basidiomycota

Genome 19, the name for each arc

Zygomycota

Genome 20, the name for each arc

interacCircos

Description

Visualization of Interactive Circos Plot

Usage

Circos(
  moduleList = CircosModuleList(),
  genome = "hg19",
  genome2 = "hg19",
  genomeFillColor = "Spectral",
  chrPad = 0.02,
  width = NULL,
  height = NULL,
  innerRadius = 216,
  outerRadius = 240,
  svgClassName = "interacCircos",
  displayGenomeBorder = TRUE,
  genomeBorderColor = "#000",
  genomeBorderSize = 0.5,
  genomeTicksDisplay = FALSE,
  genomeTicksLen = 5,
  genomeTicksColor = "#000",
  genomeTicksTextSize = "0.6em",
  genomeTicksRealLength = TRUE,
  genomeTicksTextColor = "#000",
  genomeTicksScale = 3e+07,
  genomeTicksOffset = 0,
  genomeLabelDisplay = TRUE,
  genomeLabelTextSize = "10pt",
  genomeLabelTextColor = "#000",
  genomeLabelDx = 0,
  genomeLabelDy = 0,
  compareEvent = FALSE,
  compareEventGroupGapRate = 0.1,
  compareEventGroupDistance = 0,
  zoom = TRUE,
  TEXTModuleDragEvent = FALSE,
  CNVxlink = FALSE,
  CNVMouseEvent = TRUE,
  CNVMouseClickDisplay = FALSE,
  CNVMouseClickColor = "red",
  CNVMouseClickArcOpacity = 1,
  CNVMouseClickArcStrokeColor = "#F26223",
  CNVMouseClickArcStrokeWidth = 0,
  CNVMouseClickTextFromData = "fourth",
  CNVMouseClickTextOpacity = 1,
  CNVMouseClickTextColor = "red",
  CNVMouseClickTextSize = 8,
  CNVMouseClickTextPostionX = 0,
  CNVMouseClickTextPostionY = 0,
  CNVMouseClickTextDrag = TRUE,
  CNVMouseDownDisplay = FALSE,
  CNVMouseDownColor = "green",
  CNVMouseDownArcOpacity = 1,
  CNVMouseDownArcStrokeColor = "#F26223",
  CNVMouseDownArcStrokeWidth = 0,
  CNVMouseEnterDisplay = FALSE,
  CNVMouseEnterColor = "yellow",
  CNVMouseEnterArcOpacity = 1,
  CNVMouseEnterArcStrokeColor = "#F26223",
  CNVMouseEnterArcStrokeWidth = 0,
  CNVMouseLeaveDisplay = FALSE,
  CNVMouseLeaveColor = "pink",
  CNVMouseLeaveArcOpacity = 1,
  CNVMouseLeaveArcStrokeColor = "#F26223",
  CNVMouseLeaveArcStrokeWidth = 0,
  CNVMouseMoveDisplay = FALSE,
  CNVMouseMoveColor = "red",
  CNVMouseMoveArcOpacity = 1,
  CNVMouseMoveArcStrokeColor = "#F26223",
  CNVMouseMoveArcStrokeWidth = 0,
  CNVMouseOutDisplay = FALSE,
  CNVMouseOutAnimationTime = 500,
  CNVMouseOutColor = "red",
  CNVMouseOutArcOpacity = 1,
  CNVMouseOutArcStrokeColor = "red",
  CNVMouseOutArcStrokeWidth = 0,
  CNVMouseUpDisplay = FALSE,
  CNVMouseUpColor = "grey",
  CNVMouseUpArcOpacity = 1,
  CNVMouseUpArcStrokeColor = "#F26223",
  CNVMouseUpArcStrokeWidth = 0,
  CNVMouseOverDisplay = FALSE,
  CNVMouseOverColor = "red",
  CNVMouseOverArcOpacity = 1,
  CNVMouseOverArcStrokeColor = "#F26223",
  CNVMouseOverArcStrokeWidth = 3,
  CNVMouseOverTooltipsSetting = "style1",
  CNVMouseOverTooltipsHtml = " ",
  CNVMouseOverTooltipsPosition = "absolute",
  CNVMouseOverTooltipsBackgroundColor = "white",
  CNVMouseOverTooltipsBorderStyle = "solid",
  CNVMouseOverTooltipsBorderWidth = 0,
  CNVMouseOverTooltipsPadding = "3px",
  CNVMouseOverTooltipsBorderRadius = "3px",
  CNVMouseOverTooltipsOpacity = 0.8,
  HEATMAPMouseEvent = TRUE,
  HEATMAPMouseClickDisplay = FALSE,
  HEATMAPMouseClickColor = "green",
  HEATMAPMouseClickOpacity = 1,
  HEATMAPMouseClickStrokeColor = "none",
  HEATMAPMouseClickStrokeWidth = "none",
  HEATMAPMouseDownDisplay = FALSE,
  HEATMAPMouseDownColor = "green",
  HEATMAPMouseDownOpacity = 1,
  HEATMAPMouseDownStrokeColor = "none",
  HEATMAPMouseDownStrokeWidth = "none",
  HEATMAPMouseEnterDisplay = FALSE,
  HEATMAPMouseEnterColor = "green",
  HEATMAPMouseEnterOpacity = 1,
  HEATMAPMouseEnterStrokeColor = "none",
  HEATMAPMouseEnterStrokeWidth = "none",
  HEATMAPMouseLeaveDisplay = FALSE,
  HEATMAPMouseLeaveColor = "green",
  HEATMAPMouseLeaveOpacity = 1,
  HEATMAPMouseLeaveStrokeColor = "none",
  HEATMAPMouseLeaveStrokeWidth = "none",
  HEATMAPMouseMoveDisplay = FALSE,
  HEATMAPMouseMoveColor = "green",
  HEATMAPMouseMoveOpacity = 1,
  HEATMAPMouseMoveStrokeColor = "none",
  HEATMAPMouseMoveStrokeWidth = "none",
  HEATMAPMouseOutDisplay = FALSE,
  HEATMAPMouseOutAnimationTime = 500,
  HEATMAPMouseOutColor = "green",
  HEATMAPMouseOutOpacity = 1,
  HEATMAPMouseOutStrokeColor = "none",
  HEATMAPMouseOutStrokeWidth = "none",
  HEATMAPMouseUpDisplay = FALSE,
  HEATMAPMouseUpColor = "green",
  HEATMAPMouseUpOpacity = 1,
  HEATMAPMouseUpStrokeColor = "none",
  HEATMAPMouseUpStrokeWidth = "none",
  HEATMAPMouseOverDisplay = FALSE,
  HEATMAPMouseOverColor = "none",
  HEATMAPMouseOverOpacity = 1,
  HEATMAPMouseOverStrokeColor = "none",
  HEATMAPMouseOverStrokeWidth = "none",
  HEATMAPMouseOverTooltipsSetting = "style1",
  HEATMAPMouseOverTooltipsHtml = " ",
  HEATMAPMouseOverTooltipsPosition = "absolute",
  HEATMAPMouseOverTooltipsBackgroundColor = "white",
  HEATMAPMouseOverTooltipsBorderStyle = "solid",
  HEATMAPMouseOverTooltipsBorderWidth = 0,
  HEATMAPMouseOverTooltipsPadding = "3px",
  HEATMAPMouseOverTooltipsBorderRadius = "3px",
  HEATMAPMouseOverTooltipsOpacity = 0.8,
  BUBBLExlink = FALSE,
  BUBBLEMouseEvent = TRUE,
  BUBBLEMouseClickDisplay = FALSE,
  BUBBLEMouseClickColor = "green",
  BUBBLEMouseClickOpacity = 1,
  BUBBLEMouseClickStrokeColor = "none",
  BUBBLEMouseClickStrokeWidth = "none",
  BUBBLEMouseDownDisplay = FALSE,
  BUBBLEMouseDownColor = "green",
  BUBBLEMouseDownOpacity = 1,
  BUBBLEMouseDownStrokeColor = "none",
  BUBBLEMouseDownStrokeWidth = "none",
  BUBBLEMouseEnterDisplay = FALSE,
  BUBBLEMouseEnterColor = "green",
  BUBBLEMouseEnterOpacity = 1,
  BUBBLEMouseEnterStrokeColor = "none",
  BUBBLEMouseEnterStrokeWidth = "none",
  BUBBLEMouseLeaveDisplay = FALSE,
  BUBBLEMouseLeaveColor = "green",
  BUBBLEMouseLeaveOpacity = 1,
  BUBBLEMouseLeaveStrokeColor = "none",
  BUBBLEMouseLeaveStrokeWidth = "none",
  BUBBLEMouseMoveDisplay = FALSE,
  BUBBLEMouseMoveColor = "green",
  BUBBLEMouseMoveOpacity = 1,
  BUBBLEMouseMoveStrokeColor = "none",
  BUBBLEMouseMoveStrokeWidth = "none",
  BUBBLEMouseOutDisplay = FALSE,
  BUBBLEMouseOutAnimationTime = 500,
  BUBBLEMouseOutColor = "green",
  BUBBLEMouseOutOpacity = 1,
  BUBBLEMouseOutStrokeColor = "none",
  BUBBLEMouseOutStrokeWidth = "none",
  BUBBLEMouseUpDisplay = FALSE,
  BUBBLEMouseUpColor = "green",
  BUBBLEMouseUpOpacity = 1,
  BUBBLEMouseUpStrokeColor = "none",
  BUBBLEMouseUpStrokeWidth = "none",
  BUBBLEMouseOverDisplay = FALSE,
  BUBBLEMouseOverColor = "green",
  BUBBLEMouseOverOpacity = 1,
  BUBBLEMouseOverStrokeColor = "none",
  BUBBLEMouseOverStrokeWidth = "none",
  BUBBLEMouseOverTooltipsSetting = "style1",
  BUBBLEMouseOverTooltipsHtml = " ",
  BUBBLEMouseOverTooltipsPosition = "absolute",
  BUBBLEMouseOverTooltipsBackgroundColor = "white",
  BUBBLEMouseOverTooltipsBorderStyle = "solid",
  BUBBLEMouseOverTooltipsBorderWidth = 0,
  BUBBLEMouseOverTooltipsPadding = "3px",
  BUBBLEMouseOverTooltipsBorderRadius = "3px",
  BUBBLEMouseOverTooltipsOpacity = 0.8,
  SNPxlink = FALSE,
  SNPMouseEvent = TRUE,
  SNPMouseCombinationEvent = FALSE,
  SNPMouseCombinationImageDisplay = FALSE,
  SNPMouseCombinationImageTitle = "This is image",
  SNPMouseCombinationImageTitleSize = 5,
  SNPMouseCombinationImageTitleWeight = "bold",
  SNPMouseCombinationImageTitleColor = "black",
  SNPMouseCombinationImagePositionX = 0,
  SNPMouseCombinationImagePositionY = 0,
  SNPMouseCombinationImageHeight = 200,
  SNPMouseCombinationImageWidth = 300,
  SNPMouseCombinationGraphDisplay = FALSE,
  SNPMouseCombinationGraphTitle = "This is graph",
  SNPMouseCombinationGraphTitleSize = 5,
  SNPMouseCombinationGraphTitleWeight = "bold",
  SNPMouseCombinationGraphTitleColor = "black",
  SNPMouseCombinationGraphType = "histogram",
  SNPMouseCombinationGraphPositionX = 0,
  SNPMouseCombinationGraphPositionY = 0,
  SNPMouseCombinationGraphHeight = 200,
  SNPMouseCombinationGraphWidth = 300,
  SNPMouseCombinationGraphHistogramBarColor = "blue",
  SNPMouseCombinationGraphHistogramPadding = 30,
  SNPMouseCombinationGraphHistogramPositionCorrectX = 0,
  SNPMouseCombinationGraphPieAutoColor = TRUE,
  SNPMouseCombinationGraphPieColor = c("blue", "orange"),
  SNPMouseCombinationGraphPieSize = 50,
  SNPMouseCombinationGraphPieStroke = TRUE,
  SNPMouseCombinationGraphPieStrokeColor = "black",
  SNPMouseCombinationGraphPieStrokeWidth = 1,
  SNPMouseCombinationGraphPieOpacity = 1,
  SNPMouseCombinationGraphLineType = "linear",
  SNPMouseCombinationGraphLineColor = "black",
  SNPMouseCombinationGraphLineWidth = 1,
  SNPMouseCombinationGraphLinePoint = FALSE,
  SNPMouseCombinationGraphLinePointSize = 5,
  SNPMouseCombinationGraphLinePointAutoColor = TRUE,
  SNPMouseCombinationGraphLinePointColor = c("blue", "orange"),
  SNPMouseCombinationGraphLinePointStroke = TRUE,
  SNPMouseCombinationGraphLinePointStrokeColor = "black",
  SNPMouseCombinationGraphLinePointStrokeWidth = 1,
  SNPMouseCombinationGraphLinePointOpacity = 1,
  SNPMouseCombinationGraphLinePositionCorrectX = 0,
  SNPMouseCombinationTextDisplay = FALSE,
  SNPMouseCombinationTextColor = "red",
  SNPMouseCombinationTextSize = 3,
  SNPMouseCombinationTextWeight = "bold",
  SNPMouseCombinationTextPositionCorrectX = 0,
  SNPMouseCombinationTextPositionCorrectY = 0,
  SNPMouseClickDisplay = FALSE,
  SNPMouseClickColor = "red",
  SNPMouseClickCircleSize = 4,
  SNPMouseClickCircleOpacity = 1,
  SNPMouseClickCircleStrokeColor = "#F26223",
  SNPMouseClickCircleStrokeWidth = 0,
  SNPMouseClickTextFromData = "fourth",
  SNPMouseClickTextOpacity = 1,
  SNPMouseClickTextColor = "red",
  SNPMouseClickTextSize = 8,
  SNPMouseClickTextPostionX = 1,
  SNPMouseClickTextPostionY = 10,
  SNPMouseClickTextDrag = TRUE,
  SNPMouseDownDisplay = FALSE,
  SNPMouseDownColor = "green",
  SNPMouseDownCircleSize = 4,
  SNPMouseDownCircleOpacity = 1,
  SNPMouseDownCircleStrokeColor = "#F26223",
  SNPMouseDownCircleStrokeWidth = 0,
  SNPMouseEnterDisplay = FALSE,
  SNPMouseEnterColor = "yellow",
  SNPMouseEnterCircleSize = 4,
  SNPMouseEnterCircleOpacity = 1,
  SNPMouseEnterCircleStrokeColor = "#F26223",
  SNPMouseEnterCircleStrokeWidth = 0,
  SNPMouseLeaveDisplay = FALSE,
  SNPMouseLeaveColor = "pink",
  SNPMouseLeaveCircleSize = 4,
  SNPMouseLeaveCircleOpacity = 1,
  SNPMouseLeaveCircleStrokeColor = "#F26223",
  SNPMouseLeaveCircleStrokeWidth = 0,
  SNPMouseMoveDisplay = FALSE,
  SNPMouseMoveColor = "red",
  SNPMouseMoveCircleSize = 2,
  SNPMouseMoveCircleOpacity = 1,
  SNPMouseMoveCircleStrokeColor = "#F26223",
  SNPMouseMoveCircleStrokeWidth = 0,
  SNPMouseOutDisplay = FALSE,
  SNPMouseOutAnimationTime = 500,
  SNPMouseOutColor = "red",
  SNPMouseOutCircleSize = 2,
  SNPMouseOutCircleOpacity = 1,
  SNPMouseOutCircleStrokeColor = "red",
  SNPMouseOutCircleStrokeWidth = 0,
  SNPMouseUpDisplay = FALSE,
  SNPMouseUpColor = "grey",
  SNPMouseUpCircleSize = 2,
  SNPMouseUpCircleOpacity = 1,
  SNPMouseUpCircleStrokeColor = "#F26223",
  SNPMouseUpCircleStrokeWidth = 0,
  SNPMouseOverDisplay = FALSE,
  SNPMouseOverColor = "red",
  SNPMouseOverCircleSize = 2,
  SNPMouseOverCircleOpacity = 1,
  SNPMouseOverCircleStrokeColor = "#F26223",
  SNPMouseOverCircleStrokeWidth = 3,
  SNPMouseOverTooltipsSetting = "style1",
  SNPMouseOverTooltipsHtml = " ",
  SNPMouseOverTooltipsPosition = "absolute",
  SNPMouseOverTooltipsBackgroundColor = "white",
  SNPMouseOverTooltipsBorderStyle = "solid",
  SNPMouseOverTooltipsBorderWidth = 0,
  SNPMouseOverTooltipsPadding = "3px",
  SNPMouseOverTooltipsBorderRadius = "3px",
  SNPMouseOverTooltipsOpacity = 0.8,
  LINKxlink = FALSE,
  LINKMouseEvent = TRUE,
  LINKMouseClickDisplay = FALSE,
  LINKMouseClickOpacity = 1,
  LINKMouseClickStrokeColor = "green",
  LINKMouseClickStrokeWidth = 4,
  LINKMouseDownDisplay = FALSE,
  LINKMouseDownOpacity = 1,
  LINKMouseDownStrokeColor = "none",
  LINKMouseDownStrokeWidth = "none",
  LINKMouseEnterDisplay = FALSE,
  LINKMouseEnterOpacity = 1,
  LINKMouseEnterStrokeColor = "none",
  LINKMouseEnterStrokeWidth = "none",
  LINKMouseLeaveDisplay = FALSE,
  LINKMouseLeaveOpacity = 1,
  LINKMouseLeaveStrokeColor = "none",
  LINKMouseLeaveStrokeWidth = "none",
  LINKMouseMoveDisplay = FALSE,
  LINKMouseMoveOpacity = 1,
  LINKMouseMoveStrokeColor = "none",
  LINKMouseMoveStrokeWidth = "none",
  LINKMouseOutDisplay = FALSE,
  LINKMouseOutAnimationTime = 500,
  LINKMouseOutOpacity = 1,
  LINKMouseOutStrokeColor = "none",
  LINKMouseOutStrokeWidth = "none",
  LINKMouseUpDisplay = FALSE,
  LINKMouseUpOpacity = 1,
  LINKMouseUpStrokeColor = "none",
  LINKMouseUpStrokeWidth = "none",
  LINKMouseOverDisplay = FALSE,
  LINKMouseOverOpacity = 1,
  LINKMouseOverStrokeColor = "none",
  LINKMouseOverStrokeWidth = "none",
  LINKMouseOverTooltipsSetting = "style1",
  LINKMouseOverTooltipsHtml = " ",
  LINKMouseOverTooltipsPosition = "absolute",
  LINKMouseOverTooltipsBackgroundColor = "white",
  LINKMouseOverTooltipsBorderStyle = "solid",
  LINKMouseOverTooltipsBorderWidth = 0,
  LINKMouseOverTooltipsPadding = "3px",
  LINKMouseOverTooltipsBorderRadius = "3px",
  LINKMouseOverTooltipsOpacity = 1,
  LINKLabelDragEvent = FALSE,
  CHORDMouseEvent = TRUE,
  CHORDMouseFillColorExcluded = "#FFFFFF",
  CHORDMouseClickDisplay = FALSE,
  CHORDMouseClickOpacity = 1,
  CHORDMouseClickStrokeColor = "none",
  CHORDMouseClickStrokeWidth = "none",
  CHORDMouseDownDisplay = FALSE,
  CHORDMouseDownOpacity = 1,
  CHORDMouseDownStrokeColor = "none",
  CHORDMouseDownStrokeWidth = "none",
  CHORDMouseEnterDisplay = FALSE,
  CHORDMouseEnterOpacity = 1,
  CHORDMouseEnterStrokeColor = "none",
  CHORDMouseEnterStrokeWidth = "none",
  CHORDMouseLeaveDisplay = FALSE,
  CHORDMouseLeaveOpacity = 1,
  CHORDMouseLeaveStrokeColor = "none",
  CHORDMouseLeaveStrokeWidth = "none",
  CHORDMouseMoveDisplay = FALSE,
  CHORDMouseMoveOpacity = 1,
  CHORDMouseMoveStrokeColor = "none",
  CHORDMouseMoveStrokeWidth = "none",
  CHORDMouseOutDisplay = FALSE,
  CHORDMouseOutAnimationTime = 500,
  CHORDMouseOutOpacity = 1,
  CHORDMouseOutStrokeColor = "none",
  CHORDMouseOutStrokeWidth = "none",
  CHORDMouseUpDisplay = FALSE,
  CHORDMouseUpOpacity = 1,
  CHORDMouseUpStrokeColor = "none",
  CHORDMouseUpStrokeWidth = "none",
  CHORDMouseOverDisplay = FALSE,
  CHORDMouseOverOpacity = 1,
  CHORDMouseOverStrokeColor = "none",
  CHORDMouseOverStrokeWidth = "none",
  HISTOGRAMxlink = FALSE,
  HISTOGRAMMouseEvent = TRUE,
  HISTOGRAMMouseClickDisplay = FALSE,
  HISTOGRAMMouseClickColor = "red",
  HISTOGRAMMouseClickOpacity = 1,
  HISTOGRAMMouseClickStrokeColor = "none",
  HISTOGRAMMouseClickStrokeWidth = "none",
  HISTOGRAMMouseDownDisplay = FALSE,
  HISTOGRAMMouseDownColor = "red",
  HISTOGRAMMouseDownOpacity = 1,
  HISTOGRAMMouseDownStrokeColor = "none",
  HISTOGRAMMouseDownStrokeWidth = "none",
  HISTOGRAMMouseEnterDisplay = FALSE,
  HISTOGRAMMouseEnterColor = "red",
  HISTOGRAMMouseEnterOpacity = 1,
  HISTOGRAMMouseEnterStrokeColor = "none",
  HISTOGRAMMouseEnterStrokeWidth = "none",
  HISTOGRAMMouseLeaveDisplay = FALSE,
  HISTOGRAMMouseLeaveColor = "red",
  HISTOGRAMMouseLeaveOpacity = 1,
  HISTOGRAMMouseLeaveStrokeColor = "none",
  HISTOGRAMMouseLeaveStrokeWidth = "none",
  HISTOGRAMMouseMoveDisplay = FALSE,
  HISTOGRAMMouseMoveColor = "red",
  HISTOGRAMMouseMoveOpacity = 1,
  HISTOGRAMMouseMoveStrokeColor = "none",
  HISTOGRAMMouseMoveStrokeWidth = "none",
  HISTOGRAMMouseOutDisplay = FALSE,
  HISTOGRAMMouseOutAnimationTime = 500,
  HISTOGRAMMouseOutColor = "red",
  HISTOGRAMMouseOutOpacity = 1,
  HISTOGRAMMouseOutStrokeColor = "none",
  HISTOGRAMMouseOutStrokeWidth = "none",
  HISTOGRAMMouseUpDisplay = FALSE,
  HISTOGRAMMouseUpColor = "red",
  HISTOGRAMMouseUpOpacity = 1,
  HISTOGRAMMouseUpStrokeColor = "none",
  HISTOGRAMMouseUpStrokeWidth = "none",
  HISTOGRAMMouseOverDisplay = FALSE,
  HISTOGRAMMouseOverColor = "red",
  HISTOGRAMMouseOverOpacity = 1,
  HISTOGRAMMouseOverStrokeColor = "none",
  HISTOGRAMMouseOverStrokeWidth = "none",
  HISTOGRAMMouseOverTooltipsSetting = "style1",
  HISTOGRAMMouseOverTooltipsHtml = " ",
  HISTOGRAMMouseOverTooltipsPosition = "absolute",
  HISTOGRAMMouseOverTooltipsBackgroundColor = "white",
  HISTOGRAMMouseOverTooltipsBorderStyle = "solid",
  HISTOGRAMMouseOverTooltipsBorderWidth = 0,
  HISTOGRAMMouseOverTooltipsPadding = "3px",
  HISTOGRAMMouseOverTooltipsBorderRadius = "3px",
  HISTOGRAMMouseOverTooltipsOpacity = 1,
  LINEMouseEvent = TRUE,
  LINEMouseClickDisplay = FALSE,
  LINEMouseClickLineOpacity = 1,
  LINEMouseClickLineStrokeColor = "none",
  LINEMouseClickLineStrokeWidth = "none",
  LINEMouseDownDisplay = FALSE,
  LINEMouseDownLineOpacity = 1,
  LINEMouseDownLineStrokeColor = "none",
  LINEMouseDownLineStrokeWidth = "none",
  LINEMouseEnterDisplay = FALSE,
  LINEMouseEnterLineOpacity = 1,
  LINEMouseEnterLineStrokeColor = "none",
  LINEMouseEnterLineStrokeWidth = "none",
  LINEMouseLeaveDisplay = FALSE,
  LINEMouseLeaveLineOpacity = 1,
  LINEMouseLeaveLineStrokeColor = "none",
  LINEMouseLeaveLineStrokeWidth = "none",
  LINEMouseMoveDisplay = FALSE,
  LINEMouseMoveLineOpacity = 1,
  LINEMouseMoveLineStrokeColor = "none",
  LINEMouseMoveLineStrokeWidth = "none",
  LINEMouseOutDisplay = FALSE,
  LINEMouseOutAnimationTime = 500,
  LINEMouseOutLineOpacity = 1,
  LINEMouseOutLineStrokeColor = "none",
  LINEMouseOutLineStrokeWidth = "none",
  LINEMouseUpDisplay = FALSE,
  LINEMouseUpLineOpacity = 1,
  LINEMouseUpLineStrokeColor = "none",
  LINEMouseUpLineStrokeWidth = "none",
  LINEMouseOverDisplay = FALSE,
  LINEMouseOverLineOpacity = 1,
  LINEMouseOverLineStrokeColor = "none",
  LINEMouseOverLineStrokeWidth = "none",
  LINEMouseOverTooltipsSetting = "style1",
  LINEMouseOverTooltipsHtml = " ",
  LINEMouseOverTooltipsPosition = "absolute",
  LINEMouseOverTooltipsBackgroundColor = "white",
  LINEMouseOverTooltipsBorderStyle = "solid",
  LINEMouseOverTooltipsBorderWidth = 0,
  LINEMouseOverTooltipsPadding = "3px",
  LINEMouseOverTooltipsBorderRadius = "3px",
  LINEMouseOverTooltipsOpacity = 1,
  WIGMouseEvent = TRUE,
  WIGMouseClickDisplay = FALSE,
  WIGMouseClickLineOpacity = 1,
  WIGMouseClickLineStrokeColor = "none",
  WIGMouseClickLineStrokeWidth = "none",
  WIGMouseClickFillColor = "none",
  WIGMouseDownDisplay = FALSE,
  WIGMouseDownLineOpacity = 1,
  WIGMouseDownLineStrokeColor = "none",
  WIGMouseDownLineStrokeWidth = "none",
  WIGMouseDownFillColor = "none",
  WIGMouseEnterDisplay = FALSE,
  WIGMouseEnterLineOpacity = 1,
  WIGMouseEnterLineStrokeColor = "none",
  WIGMouseEnterLineStrokeWidth = "none",
  WIGMouseEnterFillColor = "none",
  WIGMouseLeaveDisplay = FALSE,
  WIGMouseLeaveLineOpacity = 1,
  WIGMouseLeaveLineStrokeColor = "none",
  WIGMouseLeaveLineStrokeWidth = "none",
  WIGMouseLeaveFillColor = "none",
  WIGMouseMoveDisplay = FALSE,
  WIGMouseMoveLineOpacity = 1,
  WIGMouseMoveLineStrokeColor = "none",
  WIGMouseMoveLineStrokeWidth = "none",
  WIGMouseMoveFillColor = "none",
  WIGMouseOutDisplay = FALSE,
  WIGMouseOutAnimationTime = 500,
  WIGMouseOutLineOpacity = 1,
  WIGMouseOutLineStrokeColor = "none",
  WIGMouseOutLineStrokeWidth = "none",
  WIGMouseOutFillColor = "none",
  WIGMouseUpDisplay = FALSE,
  WIGMouseUpLineOpacity = 1,
  WIGMouseUpLineStrokeColor = "none",
  WIGMouseUpLineStrokeWidth = "none",
  WIGMouseUpFillColor = "none",
  WIGMouseOverDisplay = FALSE,
  WIGMouseOverLineOpacity = 1,
  WIGMouseOverLineStrokeColor = "none",
  WIGMouseOverLineStrokeWidth = "none",
  WIGMouseOverFillColor = "none",
  WIGMouseOverTooltipsSetting = "style1",
  WIGMouseOverTooltipsHtml = " ",
  WIGMouseOverTooltipsPosition = "absolute",
  WIGMouseOverTooltipsBackgroundColor = "white",
  WIGMouseOverTooltipsBorderStyle = "solid",
  WIGMouseOverTooltipsBorderWidth = 0,
  WIGMouseOverTooltipsPadding = "3px",
  WIGMouseOverTooltipsBorderRadius = "3px",
  WIGMouseOverTooltipsOpacity = 1,
  SCATTERxlink = FALSE,
  SCATTERMouseEvent = TRUE,
  SCATTERMouseClickDisplay = FALSE,
  SCATTERMouseClickColor = "red",
  SCATTERMouseClickCircleSize = 2,
  SCATTERMouseClickCircleOpacity = 1,
  SCATTERMouseClickCircleStrokeColor = "none",
  SCATTERMouseClickCircleStrokeWidth = "none",
  SCATTERMouseClickTextFromData = "fourth",
  SCATTERMouseClickTextOpacity = 1,
  SCATTERMouseClickTextColor = "red",
  SCATTERMouseClickTextSize = 8,
  SCATTERMouseClickTextPostionX = 1,
  SCATTERMouseClickTextPostionY = 10,
  SCATTERMouseClickTextDrag = TRUE,
  SCATTERMouseDownDisplay = FALSE,
  SCATTERMouseDownColor = "red",
  SCATTERMouseDownCircleSize = 2,
  SCATTERMouseDownCircleOpacity = 1,
  SCATTERMouseDownCircleStrokeColor = "none",
  SCATTERMouseDownCircleStrokeWidth = "none",
  SCATTERMouseEnterDisplay = FALSE,
  SCATTERMouseEnterColor = "red",
  SCATTERMouseEnterCircleSize = 2,
  SCATTERMouseEnterCircleOpacity = 1,
  SCATTERMouseEnterCircleStrokeColor = "none",
  SCATTERMouseEnterCircleStrokeWidth = "none",
  SCATTERMouseLeaveDisplay = FALSE,
  SCATTERMouseLeaveColor = "red",
  SCATTERMouseLeaveCircleSize = 2,
  SCATTERMouseLeaveCircleOpacity = 1,
  SCATTERMouseLeaveCircleStrokeColor = "none",
  SCATTERMouseLeaveCircleStrokeWidth = "none",
  SCATTERMouseMoveDisplay = FALSE,
  SCATTERMouseMoveColor = "red",
  SCATTERMouseMoveCircleSize = 2,
  SCATTERMouseMoveCircleOpacity = 1,
  SCATTERMouseMoveCircleStrokeColor = "none",
  SCATTERMouseMoveCircleStrokeWidth = "none",
  SCATTERMouseOutDisplay = FALSE,
  SCATTERMouseOutAnimationTime = 500,
  SCATTERMouseOutColor = "red",
  SCATTERMouseOutCircleSize = 2,
  SCATTERMouseOutCircleOpacity = 1,
  SCATTERMouseOutCircleStrokeColor = "none",
  SCATTERMouseOutCircleStrokeWidth = "none",
  SCATTERMouseUpDisplay = FALSE,
  SCATTERMouseUpColor = "red",
  SCATTERMouseUpCircleSize = 2,
  SCATTERMouseUpCircleOpacity = 1,
  SCATTERMouseUpCircleStrokeColor = "none",
  SCATTERMouseUpCircleStrokeWidth = "none",
  SCATTERMouseOverDisplay = FALSE,
  SCATTERMouseOverColor = "red",
  SCATTERMouseOverCircleSize = 2,
  SCATTERMouseOverCircleOpacity = 1,
  SCATTERMouseOverCircleStrokeColor = "none",
  SCATTERMouseOverCircleStrokeWidth = "none",
  SCATTERMouseOverTooltipsSetting = "style1",
  SCATTERMouseOverTooltipsHtml = " ",
  SCATTERMouseOverTooltipsPosition = "absolute",
  SCATTERMouseOverTooltipsBackgroundColor = "white",
  SCATTERMouseOverTooltipsBorderStyle = "solid",
  SCATTERMouseOverTooltipsBorderWidth = 0,
  SCATTERMouseOverTooltipsPadding = "3px",
  SCATTERMouseOverTooltipsBorderRadius = "3px",
  SCATTERMouseOverTooltipsOpacity = 1,
  ARCxlink = FALSE,
  ARCMouseEvent = TRUE,
  ARCMouseClickDisplay = FALSE,
  ARCMouseClickColor = "red",
  ARCMouseClickArcOpacity = 1,
  ARCMouseClickArcStrokeColor = "none",
  ARCMouseClickArcStrokeWidth = "none",
  ARCMouseClickTextFromData = "fourth",
  ARCMouseClickTextOpacity = 1,
  ARCMouseClickTextColor = "red",
  ARCMouseClickTextSize = 8,
  ARCMouseClickTextPostionX = 1,
  ARCMouseClickTextPostionY = 10,
  ARCMouseClickTextDrag = TRUE,
  ARCMouseDownDisplay = FALSE,
  ARCMouseDownColor = "red",
  ARCMouseDownArcOpacity = 1,
  ARCMouseDownArcStrokeColor = "none",
  ARCMouseDownArcStrokeWidth = "none",
  ARCMouseEnterDisplay = FALSE,
  ARCMouseEnterColor = "red",
  ARCMouseEnterArcOpacity = 1,
  ARCMouseEnterArcStrokeColor = "none",
  ARCMouseEnterArcStrokeWidth = "none",
  ARCMouseLeaveDisplay = FALSE,
  ARCMouseLeaveColor = "red",
  ARCMouseLeaveArcOpacity = 1,
  ARCMouseLeaveArcStrokeColor = "none",
  ARCMouseLeaveArcStrokeWidth = "none",
  ARCMouseMoveDisplay = FALSE,
  ARCMouseMoveColor = "red",
  ARCMouseMoveArcOpacity = 1,
  ARCMouseMoveArcStrokeColor = "none",
  ARCMouseMoveArcStrokeWidth = "none",
  ARCMouseOutDisplay = FALSE,
  ARCMouseOutAnimationTime = 500,
  ARCMouseOutColor = "red",
  ARCMouseOutArcOpacity = 1,
  ARCMouseOutArcStrokeColor = "none",
  ARCMouseOutArcStrokeWidth = "none",
  ARCMouseUpDisplay = FALSE,
  ARCMouseUpColor = "red",
  ARCMouseUpArcOpacity = 1,
  ARCMouseUpArcStrokeColor = "none",
  ARCMouseUpArcStrokeWidth = "none",
  ARCMouseOverDisplay = FALSE,
  ARCMouseOverColor = "red",
  ARCMouseOverArcOpacity = 1,
  ARCMouseOverArcStrokeColor = "none",
  ARCMouseOverArcStrokeWidth = "none",
  ARCMouseOverTooltipsSetting = "style1",
  ARCMouseOverTooltipsHtml = " ",
  ARCMouseOverTooltipsPosition = "absolute",
  ARCMouseOverTooltipsBackgroundColor = "white",
  ARCMouseOverTooltipsBorderStyle = "solid",
  ARCMouseOverTooltipsBorderWidth = 0,
  ARCMouseOverTooltipsPadding = "3px",
  ARCMouseOverTooltipsBorderRadius = "3px",
  ARCMouseOverTooltipsOpacity = 1,
  GENExlink = FALSE,
  GENEMouseEvent = TRUE,
  GENEMouseClickDisplay = FALSE,
  GENEMouseClickColor = "red",
  GENEMouseClickArcOpacity = 1,
  GENEMouseClickArcStrokeColor = "none",
  GENEMouseClickArcStrokeWidth = "none",
  GENEMouseClickTextFromData = "fourth",
  GENEMouseClickTextOpacity = 1,
  GENEMouseClickTextColor = "red",
  GENEMouseClickTextSize = 8,
  GENEMouseClickTextPostionX = 1,
  GENEMouseClickTextPostionY = 10,
  GENEMouseClickTextDrag = TRUE,
  GENEMouseDownDisplay = FALSE,
  GENEMouseDownColor = "red",
  GENEMouseDownArcOpacity = 1,
  GENEMouseDownArcStrokeColor = "none",
  GENEMouseDownArcStrokeWidth = "none",
  GENEMouseEnterDisplay = FALSE,
  GENEMouseEnterColor = "red",
  GENEMouseEnterArcOpacity = 1,
  GENEMouseEnterArcStrokeColor = "none",
  GENEMouseEnterArcStrokeWidth = "none",
  GENEMouseLeaveDisplay = FALSE,
  GENEMouseLeaveColor = "red",
  GENEMouseLeaveArcOpacity = 1,
  GENEMouseLeaveArcStrokeColor = "none",
  GENEMouseLeaveArcStrokeWidth = "none",
  GENEMouseMoveDisplay = FALSE,
  GENEMouseMoveColor = "red",
  GENEMouseMoveArcOpacity = 1,
  GENEMouseMoveArcStrokeColor = "none",
  GENEMouseMoveArcStrokeWidth = "none",
  GENEMouseOutDisplay = FALSE,
  GENEMouseOutAnimationTime = 500,
  GENEMouseOutColor = "red",
  GENEMouseOutArcOpacity = 1,
  GENEMouseOutArcStrokeColor = "none",
  GENEMouseOutArcStrokeWidth = "none",
  GENEMouseUpDisplay = FALSE,
  GENEMouseUpColor = "red",
  GENEMouseUpArcOpacity = 1,
  GENEMouseUpArcStrokeColor = "none",
  GENEMouseUpArcStrokeWidth = "none",
  GENEMouseOverDisplay = FALSE,
  GENEMouseOverColor = "red",
  GENEMouseOverArcOpacity = 1,
  GENEMouseOverArcStrokeColor = "none",
  GENEMouseOverArcStrokeWidth = "none",
  GENEMouseOverTooltipsSetting = "style1",
  GENEMouseOverTooltipsHtml = " ",
  GENEMouseOverTooltipsPosition = "absolute",
  GENEMouseOverTooltipsBackgroundColor = "white",
  GENEMouseOverTooltipsBorderStyle = "solid",
  GENEMouseOverTooltipsBorderWidth = 0,
  GENEMouseOverTooltipsPadding = "3px",
  GENEMouseOverTooltipsBorderRadius = "3px",
  GENEMouseOverTooltipsOpacity = 1,
  LOLLIPOPxlink = FALSE,
  LOLLIPOPMouseEvent = TRUE,
  LOLLIPOPMouseClickDisplay = FALSE,
  LOLLIPOPMouseClickColor = "red",
  LOLLIPOPMouseClickCircleSize = 2,
  LOLLIPOPMouseClickCircleOpacity = 1,
  LOLLIPOPMouseClickCircleStrokeColor = "none",
  LOLLIPOPMouseClickCircleStrokeWidth = "none",
  LOLLIPOPMouseClickTextFromData = "fourth",
  LOLLIPOPMouseClickTextOpacity = 1,
  LOLLIPOPMouseClickTextColor = "red",
  LOLLIPOPMouseClickTextSize = 8,
  LOLLIPOPMouseClickTextPostionX = 1,
  LOLLIPOPMouseClickTextPostionY = 10,
  LOLLIPOPMouseClickTextDrag = TRUE,
  LOLLIPOPMouseDownDisplay = FALSE,
  LOLLIPOPMouseDownColor = "red",
  LOLLIPOPMouseDownCircleSize = 2,
  LOLLIPOPMouseDownCircleOpacity = 1,
  LOLLIPOPMouseDownCircleStrokeColor = "none",
  LOLLIPOPMouseDownCircleStrokeWidth = "none",
  LOLLIPOPMouseEnterDisplay = FALSE,
  LOLLIPOPMouseEnterColor = "red",
  LOLLIPOPMouseEnterCircleSize = 2,
  LOLLIPOPMouseEnterCircleOpacity = 1,
  LOLLIPOPMouseEnterCircleStrokeColor = "none",
  LOLLIPOPMouseEnterCircleStrokeWidth = "none",
  LOLLIPOPMouseLeaveDisplay = FALSE,
  LOLLIPOPMouseLeaveColor = "red",
  LOLLIPOPMouseLeaveCircleSize = 2,
  LOLLIPOPMouseLeaveCircleOpacity = 1,
  LOLLIPOPMouseLeaveCircleStrokeColor = "none",
  LOLLIPOPMouseLeaveCircleStrokeWidth = "none",
  LOLLIPOPMouseMoveDisplay = FALSE,
  LOLLIPOPMouseMoveColor = "red",
  LOLLIPOPMouseMoveCircleSize = 2,
  LOLLIPOPMouseMoveCircleOpacity = 1,
  LOLLIPOPMouseMoveCircleStrokeColor = "none",
  LOLLIPOPMouseMoveCircleStrokeWidth = "none",
  LOLLIPOPMouseOutDisplay = FALSE,
  LOLLIPOPMouseOutAnimationTime = 500,
  LOLLIPOPMouseOutColor = "red",
  LOLLIPOPMouseOutCircleSize = 2,
  LOLLIPOPMouseOutCircleOpacity = 1,
  LOLLIPOPMouseOutCircleStrokeColor = "none",
  LOLLIPOPMouseOutCircleStrokeWidth = "none",
  LOLLIPOPMouseUpDisplay = FALSE,
  LOLLIPOPMouseUpColor = "red",
  LOLLIPOPMouseUpCircleSize = 2,
  LOLLIPOPMouseUpCircleOpacity = 1,
  LOLLIPOPMouseUpCircleStrokeColor = "none",
  LOLLIPOPMouseUpCircleStrokeWidth = "none",
  LOLLIPOPMouseOverDisplay = FALSE,
  LOLLIPOPMouseOverColor = "red",
  LOLLIPOPMouseOverCircleSize = 2,
  LOLLIPOPMouseOverCircleOpacity = 1,
  LOLLIPOPMouseOverCircleStrokeColor = "none",
  LOLLIPOPMouseOverCircleStrokeWidth = "none",
  LOLLIPOPMouseOverTooltipsSetting = "style1",
  LOLLIPOPMouseOverTooltipsHtml = " ",
  LOLLIPOPMouseOverTooltipsPosition = "absolute",
  LOLLIPOPMouseOverTooltipsBackgroundColor = "white",
  LOLLIPOPMouseOverTooltipsBorderStyle = "solid",
  LOLLIPOPMouseOverTooltipsBorderWidth = 0,
  LOLLIPOPMouseOverTooltipsPadding = "3px",
  LOLLIPOPMouseOverTooltipsBorderRadius = "3px",
  LOLLIPOPMouseOverTooltipsOpacity = 1,
  elementId = NULL,
  ...
)

Arguments

moduleList

Module list displayed in plot
genome

Could be either 'hg19', which is defaultly set to use chromosomes of hg19, or a list of chromosomes with length, for example, list("chr1"=100,"chr2"=200)
genome2

Second genome when compare module is applied, format is same as genome
genomeFillColor

Could be either a color palette from RColorBrewer, or a list of color name, for example, list("yellow","rgb(1,255,255)")
chrPad

Distance between each chromosome, default is 0.04
width, height

The width and height for svg element, could be px or percent or auto
innerRadius

Default 216, Inner radius of chromosome
outerRadius

Default 240, Outer radius of chromosome
svgClassName

The svg class name
displayGenomeBorder

Whether display a border for genome track or not
genomeBorderColor, genomeBorderSize

The color and size for border of genome
genomeTicksDisplay

Whether display the ticks for genome track
genomeTicksLen, genomeTicksColor, genomeTicksTextSize, genomeTicksTextColor, genomeTicksScale, genomeTicksRealLength, genomeTicksOffset

arameters only works when genomeTicksDisplay is TRUE and their details are available on document
genomeLabelDisplay, genomeLabelTextSize, genomeLabelTextColor, genomeLabelDx, genomeLabelDy

Whether display the label for chromosome panel. Other parameters only works when genomeTicksDisplay is TRUE and their details are available on document
compareEvent

Default False, open/not COMPARE module
compareEventGroupGapRate

Default 0.1, control the two-side gap rate on each group of genome
compareEventGroupDistance

Default 0, distance between two groups of genome
zoom

Whether or not the plot is zoomable?
TEXTModuleDragEvent

Are text annotations draggable?
CNVxlink

Default False, add/not xlink for CNV module
CNVMouseEvent

Default True, open/not open mouse event of CNV module
CNVMouseClickDisplay

Default False, show/not the tooltip when mouse click on a CNV point
CNVMouseClickColor

Color when mouse clicking
CNVMouseClickArcOpacity

Arc opacity when mouse clicking the element
CNVMouseClickArcStrokeColor

Arc stroke color when mouse clicking the element
CNVMouseClickArcStrokeWidth

Arc stroke width when mouse clicking the element
CNVMouseClickTextFromData

Text column when mouse clicking the element
CNVMouseClickTextOpacity

Text opacity when mouse clicking the element
CNVMouseClickTextColor

Text color when mouse clicking the element
CNVMouseClickTextSize

Text size when mouse clicking the element
CNVMouseClickTextPostionX, CNVMouseClickTextPostionY

Text coordinates when mouse clicking the element
CNVMouseClickTextDrag

Whether text is draggable when mouse clicking the element
CNVMouseDownDisplay

Default False, show/not the tooltip when mouse click down a CNV point
CNVMouseDownColor

Color when mouse moving down the element
CNVMouseDownArcOpacity

Arc opacity when mouse moving down the element
CNVMouseDownArcStrokeColor

Arc stroke color when mouse moving down the element
CNVMouseDownArcStrokeWidth

Arc stroke width when mouse moving down the element
CNVMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a CNV point
CNVMouseEnterColor

Color when mouse entering the element
CNVMouseEnterArcOpacity

Arc opacity when mouse entering the element
CNVMouseEnterArcStrokeColor

Arc stroke color when mouse entering the element
CNVMouseEnterArcStrokeWidth

Arc stroke width when mouse entering the element
CNVMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a CNV point
CNVMouseLeaveColor

Color when mouse leaving the element
CNVMouseLeaveArcOpacity

Arc opacity when mouse leaving the element
CNVMouseLeaveArcStrokeColor

Arc stroke color when mouse leaving the element
CNVMouseLeaveArcStrokeWidth

Arc stroke width when mouse leaving the element
CNVMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a CNV point
CNVMouseMoveColor

Color when mouse moving in the element
CNVMouseMoveArcOpacity

Arc opacity when mouse moving in the element
CNVMouseMoveArcStrokeColor

Arc stroke color when mouse moving in the element
CNVMouseMoveArcStrokeWidth

Arc stroke width when mouse moving in the element
CNVMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a CNV point anymore
CNVMouseOutAnimationTime

Animation time when mouse moving out the element
CNVMouseOutColor

Color when mouse moving out the element
CNVMouseOutArcOpacity

Arc opacity when mouse moving out the element
CNVMouseOutArcStrokeColor

Arc stroke color when mouse moving out the element
CNVMouseOutArcStrokeWidth

Arc stroke width when mouse moving out the element
CNVMouseUpDisplay

Default False, show/not the tooltip when mouse click up a CNV point
CNVMouseUpColor

Color when mouse moving up the element
CNVMouseUpArcOpacity

Arc opacity when mouse clicking the element
CNVMouseUpArcStrokeColor

Arc stroke color when mouse clicking the element
CNVMouseUpArcStrokeWidth

Arc stroke width when mouse clicking the element
CNVMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a CNV point
CNVMouseOverColor

Color when mouse moving over the element
CNVMouseOverArcOpacity

Arc opacity when mouse moving over the element
CNVMouseOverArcStrokeColor

Arc stroke color when mouse moving over the element
CNVMouseOverArcStrokeWidth

Arc stroke width when mouse moving over the element
CNVMouseOverTooltipsSetting

Default "style1"
CNVMouseOverTooltipsHtml

Default " "
CNVMouseOverTooltipsPosition

Default "absolute"
CNVMouseOverTooltipsBackgroundColor

Default "white"
CNVMouseOverTooltipsBorderStyle

Default "solid"
CNVMouseOverTooltipsBorderWidth

Default 0
CNVMouseOverTooltipsPadding

Default "3px"
CNVMouseOverTooltipsBorderRadius

Default "3px"
CNVMouseOverTooltipsOpacity

Default 0.8
HEATMAPMouseEvent

Default True, open/not open mouse event of HEATMAP module
HEATMAPMouseClickDisplay

Default False, show/not the tooltip when mouse click on a HEATMAP point
HEATMAPMouseClickColor

Color when mouse clicking
HEATMAPMouseClickOpacity

Opacity when mouse clicking
HEATMAPMouseClickStrokeColor

Stroke color when mouse clicking
HEATMAPMouseClickStrokeWidth

Stroke width when mouse clicking
HEATMAPMouseDownDisplay

Default False, show/not the tooltip when mouse click down a HEATMAP point
HEATMAPMouseDownColor

Color when mouse moving down the element
HEATMAPMouseDownOpacity

Opacity when mouse moving down the element
HEATMAPMouseDownStrokeColor

Stroke color when mouse moving down the element
HEATMAPMouseDownStrokeWidth

Stroke width when mouse moving down the element
HEATMAPMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a HEATMAP point
HEATMAPMouseEnterColor

Color when mouse entering the element
HEATMAPMouseEnterOpacity

Opacity when mouse entering the element
HEATMAPMouseEnterStrokeColor

Stroke color when mouse entering the element
HEATMAPMouseEnterStrokeWidth

Stroke width when mouse entering the element
HEATMAPMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a HEATMAP point
HEATMAPMouseLeaveColor

Color when mouse leaving the element
HEATMAPMouseLeaveOpacity

Opacity when mouse leaving the element
HEATMAPMouseLeaveStrokeColor

Stroke color when mouse leaving the element
HEATMAPMouseLeaveStrokeWidth

Stroke width when mouse leaving the element
HEATMAPMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a HEATMAP point
HEATMAPMouseMoveColor

Color when mouse moving in the element
HEATMAPMouseMoveOpacity

Opacity when mouse moving in the element
HEATMAPMouseMoveStrokeColor

Stroke color when mouse moving in the element
HEATMAPMouseMoveStrokeWidth

Stroke width when mouse moving in the element
HEATMAPMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a HEATMAP point anymore
HEATMAPMouseOutAnimationTime

Animation time when mouse moving out the element
HEATMAPMouseOutColor

Color when mouse moving out the element
HEATMAPMouseOutOpacity

Opacity when mouse moving out the element
HEATMAPMouseOutStrokeColor

Stroke color when mouse moving out the element
HEATMAPMouseOutStrokeWidth

Stroke width when mouse moving out the element
HEATMAPMouseUpDisplay

Default False, show/not the tooltip when mouse click up a HEATMAP point
HEATMAPMouseUpColor

Color when mouse moving up the element
HEATMAPMouseUpOpacity

Opacity when mouse moving up the element
HEATMAPMouseUpStrokeColor

Stroke color when mouse moving up the element
HEATMAPMouseUpStrokeWidth

Stroke width when mouse moving up the element
HEATMAPMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a HEATMAP point
HEATMAPMouseOverColor

Color when mouse moving over the element
HEATMAPMouseOverOpacity

Opacity when mouse moving over the element
HEATMAPMouseOverStrokeColor

Stroke color when mouse moving over the element
HEATMAPMouseOverStrokeWidth

Stroke width when mouse moving over the element
HEATMAPMouseOverTooltipsSetting

Default "style1"
HEATMAPMouseOverTooltipsHtml

Default " "
HEATMAPMouseOverTooltipsPosition

Default "absolute"
HEATMAPMouseOverTooltipsBackgroundColor

Default "white"
HEATMAPMouseOverTooltipsBorderStyle

Default "solid"
HEATMAPMouseOverTooltipsBorderWidth

Default 0
HEATMAPMouseOverTooltipsPadding

Default "3px"
HEATMAPMouseOverTooltipsBorderRadius

Default "3px"
HEATMAPMouseOverTooltipsOpacity

Default 0.8
BUBBLExlink

Default False, add/not xlink for BUBBLE module
BUBBLEMouseEvent

Default True, open/not open mouse event of BUBBLE module
BUBBLEMouseClickDisplay

Default False, show/not the tooltip when mouse click on a BUBBLE point
BUBBLEMouseClickColor

Color when mouse clicking
BUBBLEMouseClickOpacity

Opacity when mouse clicking
BUBBLEMouseClickStrokeColor

Stroke color when mouse clicking
BUBBLEMouseClickStrokeWidth

Stroke width when mouse clicking
BUBBLEMouseDownDisplay

Default False, show/not the tooltip when mouse click down a BUBBLE point
BUBBLEMouseDownColor

Color when mouse moving down the element
BUBBLEMouseDownOpacity

Opacity when mouse moving down the element
BUBBLEMouseDownStrokeColor

Stroke color when mouse moving down the element
BUBBLEMouseDownStrokeWidth

Stroke width when mouse moving down the element
BUBBLEMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a BUBBLE point
BUBBLEMouseEnterColor

Color when mouse entering the element
BUBBLEMouseEnterOpacity

Opacity when mouse entering the element
BUBBLEMouseEnterStrokeColor

Stroke color when mouse entering the element
BUBBLEMouseEnterStrokeWidth

Stroke width when mouse entering the element
BUBBLEMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a BUBBLE point
BUBBLEMouseLeaveColor

Color when mouse leaving the element
BUBBLEMouseLeaveOpacity

Opacity when mouse leaving the element
BUBBLEMouseLeaveStrokeColor

Stroke color when mouse leaving the element
BUBBLEMouseLeaveStrokeWidth

Stroke width when mouse leaving the element
BUBBLEMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a BUBBLE point
BUBBLEMouseMoveColor

Color when mouse moving in the element
BUBBLEMouseMoveOpacity

Opacity when mouse moving in the element
BUBBLEMouseMoveStrokeColor

Stroke color when mouse moving in the element
BUBBLEMouseMoveStrokeWidth

Stroke width when mouse moving in the element
BUBBLEMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a BUBBLE point anymore
BUBBLEMouseOutAnimationTime

Animation time when mouse moving out the element
BUBBLEMouseOutColor

Color when mouse moving out the element
BUBBLEMouseOutOpacity

Opacity when mouse moving out the element
BUBBLEMouseOutStrokeColor

Stroke color when mouse moving out the element
BUBBLEMouseOutStrokeWidth

Stroke width when mouse moving out the element
BUBBLEMouseUpDisplay

Default False, show/not the tooltip when mouse click up a BUBBLE point
BUBBLEMouseUpColor

Color when mouse moving up the element
BUBBLEMouseUpOpacity

Opacity when mouse moving up the element
BUBBLEMouseUpStrokeColor

Stroke color when mouse moving up the element
BUBBLEMouseUpStrokeWidth

Stroke width when mouse moving up the element
BUBBLEMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a BUBBLE point
BUBBLEMouseOverColor

Color when mouse moving over the element
BUBBLEMouseOverOpacity

Opacity when mouse moving over the element
BUBBLEMouseOverStrokeColor

Stroke color when mouse moving over the element
BUBBLEMouseOverStrokeWidth

Stroke width when mouse moving over the element
BUBBLEMouseOverTooltipsSetting

Default "style1"
BUBBLEMouseOverTooltipsHtml

Default " "
BUBBLEMouseOverTooltipsPosition

Default "absolute"
BUBBLEMouseOverTooltipsBackgroundColor

Default "white"
BUBBLEMouseOverTooltipsBorderStyle

Default "solid"
BUBBLEMouseOverTooltipsBorderWidth

Default 0
BUBBLEMouseOverTooltipsPadding

Default "3px"
BUBBLEMouseOverTooltipsBorderRadius

Default "3px"
BUBBLEMouseOverTooltipsOpacity

Default 0.8
SNPxlink

Default False, add/not xlink for SNP module
SNPMouseEvent

Default True, open/not open mouse event of SNP module
SNPMouseCombinationEvent

Default False, open/not COMBINATION module for SNP module
SNPMouseCombinationImageDisplay

Defalut False, open/not image display in COMBINATION module for SNP module
SNPMouseCombinationImageTitle

Title of the image
SNPMouseCombinationImageTitleSize, SNPMouseCombinationImageTitleWeight, SNPMouseCombinationImageTitleColor

Size, weight and color of the title
SNPMouseCombinationImagePositionX, SNPMouseCombinationImagePositionY

Coordinates for image
SNPMouseCombinationImageHeight, SNPMouseCombinationImageWidth

Height and width of image
SNPMouseCombinationGraphDisplay

Defalut False, open/not graph display in COMBINATION module for SNP module
SNPMouseCombinationGraphTitle

Title of the graph
SNPMouseCombinationGraphTitleSize, SNPMouseCombinationGraphTitleWeight, SNPMouseCombinationGraphTitleColor

Size, weight and color of the title
SNPMouseCombinationGraphType

Type of graph
SNPMouseCombinationGraphPositionX, SNPMouseCombinationGraphPositionY

Coordinates for graph
SNPMouseCombinationGraphHeight, SNPMouseCombinationGraphWidth

Height and width for graph
SNPMouseCombinationGraphHistogramBarColor

Bar color of histogram graph
SNPMouseCombinationGraphHistogramPadding

Padding between bar of histogram graph
SNPMouseCombinationGraphHistogramPositionCorrectX

Correction distance of X axis in histogram
SNPMouseCombinationGraphPieAutoColor

Whether use auto color for pie graph or not
SNPMouseCombinationGraphPieColor

Color for pie graph if auto color is false
SNPMouseCombinationGraphPieSize

Size of pie graph
SNPMouseCombinationGraphPieStroke

Whether each pie has a stroke or not
SNPMouseCombinationGraphPieStrokeColor, SNPMouseCombinationGraphPieStrokeWidth

The stroke color and width for pie graph
SNPMouseCombinationGraphPieOpacity

Opacity for pie graph
SNPMouseCombinationGraphLineType, SNPMouseCombinationGraphLineColor, SNPMouseCombinationGraphLineWidth

Line type, color and width for line graph
SNPMouseCombinationGraphLinePoint

Whether display the broken point in line graph
SNPMouseCombinationGraphLinePointSize

Size of broken point
SNPMouseCombinationGraphLinePointAutoColor

Whether display the broken point in auto color
SNPMouseCombinationGraphLinePointColor

Color for broken point if auto color is false
SNPMouseCombinationGraphLinePointStroke

Whether display the broken point stroke
SNPMouseCombinationGraphLinePointStrokeColor, SNPMouseCombinationGraphLinePointStrokeWidth

The stroke color and width for broken point
SNPMouseCombinationGraphLinePointOpacity

Opacity for broken line
SNPMouseCombinationGraphLinePositionCorrectX

Correction distance of X axis for line
SNPMouseCombinationTextDisplay

Defalut False, open/not text display in COMBINATION module for SNP module
SNPMouseCombinationTextColor, SNPMouseCombinationTextSize, SNPMouseCombinationTextWeight

The color, size and weight for text
SNPMouseCombinationTextPositionCorrectX, SNPMouseCombinationTextPositionCorrectY

The coordinates for text
SNPMouseClickDisplay

Default False, show/not the tooltip when mouse click on a SNP point
SNPMouseClickColor

Color after clicking the element
SNPMouseClickCircleSize

Circle size after clicking the element
SNPMouseClickCircleOpacity

Opacity after clicking the element
SNPMouseClickCircleStrokeColor

Stroke color after clicking the element
SNPMouseClickCircleStrokeWidth

Stroke width after clicking the element
SNPMouseClickTextFromData

First,second,third,fourth column data click to show
SNPMouseClickTextOpacity

Text opacity after clicking the element
SNPMouseClickTextColor

Text color after clicking the element
SNPMouseClickTextSize

Text size after clicking the element
SNPMouseClickTextPostionX, SNPMouseClickTextPostionY

Text coordinate after clicking the element
SNPMouseClickTextDrag

Whether text is draggable for element
SNPMouseDownDisplay

Default False, show/not the tooltip when mouse click down a SNP point
SNPMouseDownColor

Color after mouse moving down the element
SNPMouseDownCircleSize

Circle size after mouse moving down the element
SNPMouseDownCircleOpacity

Circle opacity after mouse moving down the element
SNPMouseDownCircleStrokeColor

Circle stroke color after mouse moving down the element
SNPMouseDownCircleStrokeWidth

Circle stroke width after mouse moving down the element
SNPMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a SNP point
SNPMouseEnterColor

Color after mouse entering enter the element
SNPMouseEnterCircleSize

Circle size after mouse entering the element
SNPMouseEnterCircleOpacity

Circle opacity after mouse entering the element
SNPMouseEnterCircleStrokeColor

Circle stroke color after mouse entering the element
SNPMouseEnterCircleStrokeWidth

Circle stroke width after mouse entering the element
SNPMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a SNP point
SNPMouseLeaveColor

Color after mouse leaving the element
SNPMouseLeaveCircleSize

Circle size after mouse leaving the element
SNPMouseLeaveCircleOpacity

Circle opacity after mouse leaving the element
SNPMouseLeaveCircleStrokeColor

Circle stroke color after mouse leaving the element
SNPMouseLeaveCircleStrokeWidth

Circle stroke width after mouse leaving the element
SNPMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a SNP point
SNPMouseMoveColor

Color after mouse moving in the element
SNPMouseMoveCircleSize

Circle size after mouse moving in the element
SNPMouseMoveCircleOpacity

Circle opacity after mouse moving in the element
SNPMouseMoveCircleStrokeColor

Circle stroke color after mouse moving in the element
SNPMouseMoveCircleStrokeWidth

Circle stroke width after mouse moving in the element
SNPMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a SNP point anymore
SNPMouseOutAnimationTime

Animation time when mouse moving over the element
SNPMouseOutColor

Color when mouse moving over the element
SNPMouseOutCircleSize

Circle size when mouse moving over the element
SNPMouseOutCircleOpacity

Opacity when mouse moving over the element
SNPMouseOutCircleStrokeColor

Stroke color when mouse moving over the element
SNPMouseOutCircleStrokeWidth

Stroke width when mouse moving over the element
SNPMouseUpDisplay

Default False, show/not the tooltip when mouse click up a SNP point
SNPMouseUpColor

Color after mouse moving up the element
SNPMouseUpCircleSize

Circle size after mouse moving up the element
SNPMouseUpCircleOpacity

Circle opacity after mouse moving up the element
SNPMouseUpCircleStrokeColor

Circle stroke color after mouse moving up the element
SNPMouseUpCircleStrokeWidth

Circle stroke width after mouse moving up the element
SNPMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a SNP point
SNPMouseOverColor

Color after mouse moving over the element
SNPMouseOverCircleSize

Circle size after mouse moving over the element
SNPMouseOverCircleOpacity

Circle opacity after mouse moving over the element
SNPMouseOverCircleStrokeColor

Circle stroke color after mouse moving over the element
SNPMouseOverCircleStrokeWidth

Circle stroke width after mouse moving over the element
SNPMouseOverTooltipsSetting

Default "chr : "
SNPMouseOverTooltipsHtml

Default " "
SNPMouseOverTooltipsPosition

Position for tooltips when mouse moving over
SNPMouseOverTooltipsBackgroundColor

Background color for tooltips when mouse moving over
SNPMouseOverTooltipsBorderStyle

Border style for tooltips when mouse moving over
SNPMouseOverTooltipsBorderWidth

Border width for tooltips when mouse moving over
SNPMouseOverTooltipsPadding

Padding for tooltips when mouse moving over
SNPMouseOverTooltipsBorderRadius

Border radius for tooltips when mouse moving over
SNPMouseOverTooltipsOpacity

Opacity for tooltips when mouse moving over
LINKxlink

Default False, add/not xlink for LINK module
LINKMouseEvent

Default True, open/not open mouse event of LINK module
LINKMouseClickDisplay

Default False, show/not the tooltip when mouse click on a LINK point
LINKMouseClickOpacity

Opacity when mouse clicking
LINKMouseClickStrokeColor

Stroke color when mouse clicking
LINKMouseClickStrokeWidth

Stroke width when mouse clicking
LINKMouseDownDisplay

Default False, show/not the tooltip when mouse click down a LINK point
LINKMouseDownOpacity

Opacity when mouse moving down the element
LINKMouseDownStrokeColor

Stroke color when mouse moving down the element
LINKMouseDownStrokeWidth

Stroke width when mouse moving down the element
LINKMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a LINK point
LINKMouseEnterOpacity

Opacity when mouse entering the element
LINKMouseEnterStrokeColor

Stroke color when mouse entering the element
LINKMouseEnterStrokeWidth

Stroke width when mouse entering the element
LINKMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a LINK point
LINKMouseLeaveOpacity

Opacity when mouse leaving the element
LINKMouseLeaveStrokeColor

Stroke color when mouse leaving the element
LINKMouseLeaveStrokeWidth

Stroke width when mouse leaving the element
LINKMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a LINK point
LINKMouseMoveOpacity

Opacity when mouse moving in the element
LINKMouseMoveStrokeColor

Stroke color when mouse moving in the element
LINKMouseMoveStrokeWidth

Stroke width when mouse moving in the element
LINKMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a LINK point anymore
LINKMouseOutAnimationTime

Animation time when mouse moving out the element
LINKMouseOutOpacity

Opacity when mouse moving out the element
LINKMouseOutStrokeColor

Stroke color when mouse moving out the element
LINKMouseOutStrokeWidth

Stroke width when mouse moving out the element
LINKMouseUpDisplay

Default False, show/not the tooltip when mouse click up a LINK point
LINKMouseUpOpacity

Opacity when mouse moving up the element
LINKMouseUpStrokeColor

Stroke color when mouse moving up the element
LINKMouseUpStrokeWidth

Stroke width when mouse moving up the element
LINKMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a LINK point
LINKMouseOverOpacity

Opacity when mouse moving over the element
LINKMouseOverStrokeColor

Stroke color when mouse moving over the element
LINKMouseOverStrokeWidth

Stroke width when mouse moving over the element
LINKMouseOverTooltipsSetting

Default "style1"
LINKMouseOverTooltipsHtml

Default " "
LINKMouseOverTooltipsPosition

Default "absolute"
LINKMouseOverTooltipsBackgroundColor

Default "white"
LINKMouseOverTooltipsBorderStyle

Default "solid"
LINKMouseOverTooltipsBorderWidth

Default 0
LINKMouseOverTooltipsPadding

Default "3px"
LINKMouseOverTooltipsBorderRadius

Default "3px"
LINKMouseOverTooltipsOpacity

Default 0.8
LINKLabelDragEvent

Defalut False, draggable for the label of LINK module
CHORDMouseEvent

Default True, open/not open mouse event of CHORD module from NG-Circos
CHORDMouseFillColorExcluded

A type of color in character, chord in this color will be hided
CHORDMouseClickDisplay

Default False, show/not the tooltip when mouse click on a CHORD point
CHORDMouseClickOpacity

Opacity when mouse clicking
CHORDMouseClickStrokeColor

Stroke color when mouse clicking
CHORDMouseClickStrokeWidth

Stroke width when mouse clicking
CHORDMouseDownDisplay

Default False, show/not the tooltip when mouse click down a CHORD point
CHORDMouseDownOpacity

Opacity when mouse moving down the element
CHORDMouseDownStrokeColor

Stroke color when mouse moving down the element
CHORDMouseDownStrokeWidth

Stroke width when mouse moving down the element
CHORDMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a CHORD point
CHORDMouseEnterOpacity

Opacity when mouse entering the element
CHORDMouseEnterStrokeColor

Stroke color when mouse entering the element
CHORDMouseEnterStrokeWidth

Stroke width when mouse entering the element
CHORDMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a CHORD point
CHORDMouseLeaveOpacity

Opacity when mouse leaving the element
CHORDMouseLeaveStrokeColor

Stroke color when mouse leaving the element
CHORDMouseLeaveStrokeWidth

Stroke width when mouse leaving the element
CHORDMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a CHORD point
CHORDMouseMoveOpacity

Opacity when mouse moving in the element
CHORDMouseMoveStrokeColor

Stroke color when mouse moving in the element
CHORDMouseMoveStrokeWidth

Stroke width when mouse moving in the element
CHORDMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a CHORD point anymore
CHORDMouseOutAnimationTime

Animation time when mouse moving out the element
CHORDMouseOutOpacity

Opacity when mouse moving out the element
CHORDMouseOutStrokeColor

Stroke color when mouse moving out the element
CHORDMouseOutStrokeWidth

Stroke width when mouse moving out the element
CHORDMouseUpDisplay

Default False, show/not the tooltip when mouse click up a CHORD point
CHORDMouseUpOpacity

Opacity when mouse moving up the element
CHORDMouseUpStrokeColor

Stroke color when mouse moving up the element
CHORDMouseUpStrokeWidth

Stroke width when mouse moving up the element
CHORDMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a CHORD point
CHORDMouseOverOpacity

Opacity when mouse moving over the element
CHORDMouseOverStrokeColor

Stroke color when mouse moving over the element
CHORDMouseOverStrokeWidth

Stroke width when mouse moving over the element
HISTOGRAMxlink

Default False, add/not xlink for HISTOGRAM module
HISTOGRAMMouseEvent

Default True, open/not open mouse event of HISTOGRAM module
HISTOGRAMMouseClickDisplay

Default False, show/not the tooltip when mouse click on a HISTOGRAM point
HISTOGRAMMouseClickColor

Color when mouse clicking
HISTOGRAMMouseClickOpacity

Opacity when mouse clicking
HISTOGRAMMouseClickStrokeColor

Stroke color when mouse clicking
HISTOGRAMMouseClickStrokeWidth

Stroke width when mouse clicking
HISTOGRAMMouseDownDisplay

Default False, show/not the tooltip when mouse click down a HISTOGRAM point
HISTOGRAMMouseDownColor

Color when mouse moving down the element
HISTOGRAMMouseDownOpacity

Opacity when mouse moving up the element
HISTOGRAMMouseDownStrokeColor

Stroke color when mouse moving up the element
HISTOGRAMMouseDownStrokeWidth

Stroke width when mouse moving up the element
HISTOGRAMMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a HISTOGRAM point
HISTOGRAMMouseEnterColor

Color when mouse entering the element
HISTOGRAMMouseEnterOpacity

Opacity when mouse entering the element
HISTOGRAMMouseEnterStrokeColor

Stroke color when mouse entering the element
HISTOGRAMMouseEnterStrokeWidth

Stroke width when mouse entering the element
HISTOGRAMMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a HISTOGRAM point
HISTOGRAMMouseLeaveColor

Color when mouse leaving the element
HISTOGRAMMouseLeaveOpacity

Opacity when mouse leaving the element
HISTOGRAMMouseLeaveStrokeColor

Stroke color when mouse leaving the element
HISTOGRAMMouseLeaveStrokeWidth

Stroke width when mouse leaving the element
HISTOGRAMMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a HISTOGRAM point
HISTOGRAMMouseMoveColor

Color when mouse moving in the element
HISTOGRAMMouseMoveOpacity

Opacity when mouse moving in the element
HISTOGRAMMouseMoveStrokeColor

Stroke color when mouse moving in the element
HISTOGRAMMouseMoveStrokeWidth

Stroke width when mouse moving in the element
HISTOGRAMMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a HISTOGRAM point anymore
HISTOGRAMMouseOutAnimationTime

Animation time when mouse moving out the element
HISTOGRAMMouseOutColor

Color when mouse moving out the element
HISTOGRAMMouseOutOpacity

Opacity when mouse moving out the element
HISTOGRAMMouseOutStrokeColor

Stroke color when mouse moving out the element
HISTOGRAMMouseOutStrokeWidth

Stroke width when mouse moving out the element
HISTOGRAMMouseUpDisplay

Default False, show/not the tooltip when mouse click up a HISTOGRAM point
HISTOGRAMMouseUpColor

Color when mouse moving up the element
HISTOGRAMMouseUpOpacity

Opacity when mouse moving up the element
HISTOGRAMMouseUpStrokeColor

Stroke color when mouse moving up the element
HISTOGRAMMouseUpStrokeWidth

Stroke width when mouse moving up the element
HISTOGRAMMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a HISTOGRAM point
HISTOGRAMMouseOverColor

Color when mouse moving over the element
HISTOGRAMMouseOverOpacity

Opacity when mouse moving over the element
HISTOGRAMMouseOverStrokeColor

Stroke color when mouse moving over the element
HISTOGRAMMouseOverStrokeWidth

Stroke width when mouse moving over the element
HISTOGRAMMouseOverTooltipsSetting

Default "style1"
HISTOGRAMMouseOverTooltipsHtml

Default " "
HISTOGRAMMouseOverTooltipsPosition

Default "absolute"
HISTOGRAMMouseOverTooltipsBackgroundColor

Default "white"
HISTOGRAMMouseOverTooltipsBorderStyle

Default "solid"
HISTOGRAMMouseOverTooltipsBorderWidth

Default 0
HISTOGRAMMouseOverTooltipsPadding

Default "3px"
HISTOGRAMMouseOverTooltipsBorderRadius

Default "3px"
HISTOGRAMMouseOverTooltipsOpacity

Default 0.8
LINEMouseEvent

Default True, open/not open mouse event of LINE module
LINEMouseClickDisplay

Default False, show/not the tooltip when mouse click on a LINE point
LINEMouseClickLineOpacity

Line opacity when mouse clicking the element
LINEMouseClickLineStrokeColor

Stroke color when mouse clicking the element
LINEMouseClickLineStrokeWidth

Stroke width when mouse clicking the element
LINEMouseDownDisplay

Default False, show/not the tooltip when mouse click down a LINE point
LINEMouseDownLineOpacity

Line opacity when mouse moving down the element
LINEMouseDownLineStrokeColor

Stroke color when mouse moving down the element
LINEMouseDownLineStrokeWidth

Stroke width when mouse moving down the element
LINEMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a LINE point
LINEMouseEnterLineOpacity

Line opacity when mouse entering the element
LINEMouseEnterLineStrokeColor

Stroke color when mouse entering the element
LINEMouseEnterLineStrokeWidth

Stroke width when mouse entering the element
LINEMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a LINE point
LINEMouseLeaveLineOpacity

Line opacity when mouse leaving the element
LINEMouseLeaveLineStrokeColor

Stroke color when mouse leaving the element
LINEMouseLeaveLineStrokeWidth

Stroke width when mouse leaving the element
LINEMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a LINE point
LINEMouseMoveLineOpacity

Line opacity when mouse moving in the element
LINEMouseMoveLineStrokeColor

Stroke color when mouse moving in the element
LINEMouseMoveLineStrokeWidth

Stroke width when mouse moving in the element
LINEMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a LINE point anymore
LINEMouseOutAnimationTime

Animation time when mouse moving out the element
LINEMouseOutLineOpacity

Line opacity when mouse moving out the element
LINEMouseOutLineStrokeColor

Stroke color when mouse moving out the element
LINEMouseOutLineStrokeWidth

Stroke width when mouse moving out the element
LINEMouseUpDisplay

Default False, show/not the tooltip when mouse click up a LINE point
LINEMouseUpLineOpacity

Line opacity when mouse moving up the element
LINEMouseUpLineStrokeColor

Stroke color when mouse moving up the element
LINEMouseUpLineStrokeWidth

Stroke width when mouse moving up the element
LINEMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a LINE point
LINEMouseOverLineOpacity

Line opacity when mouse moving over the element
LINEMouseOverLineStrokeColor

Stroke color when mouse moving over the element
LINEMouseOverLineStrokeWidth

Stroke width when mouse moving over the element
LINEMouseOverTooltipsSetting

Default "style1"
LINEMouseOverTooltipsHtml

Default " "
LINEMouseOverTooltipsPosition

Default "absolute"
LINEMouseOverTooltipsBackgroundColor

Default "white"
LINEMouseOverTooltipsBorderStyle

Default "solid"
LINEMouseOverTooltipsBorderWidth

Default 0
LINEMouseOverTooltipsPadding

Default "3px"
LINEMouseOverTooltipsBorderRadius

Default "3px"
LINEMouseOverTooltipsOpacity

Default 0.8
WIGMouseEvent

Default True, open/not open mouse event of WIG module
WIGMouseClickDisplay

Default False, show/not the tooltip when mouse click on a WIG point
WIGMouseClickLineOpacity

Line opacity when mouse clicking the element
WIGMouseClickLineStrokeColor

Stroke color when mouse clicking the element
WIGMouseClickLineStrokeWidth

Stroke width when mouse clicking the element
WIGMouseClickFillColor

Filling color when mouse clicking the element
WIGMouseDownDisplay

Default False, show/not the tooltip when mouse click down a WIG point
WIGMouseDownLineOpacity

Line opacity when mouse moving down the element
WIGMouseDownLineStrokeColor

Stroke color when mouse moving down the element
WIGMouseDownLineStrokeWidth

Stroke width when mouse moving down the element
WIGMouseDownFillColor

Filling color when mouse moving down the element
WIGMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a WIG point
WIGMouseEnterLineOpacity

Line opacity when mouse entering the element
WIGMouseEnterLineStrokeColor

Stroke color when mouse entering the element
WIGMouseEnterLineStrokeWidth

Stroke width when mouse entering the element
WIGMouseEnterFillColor

Filling color when mouse entering the element
WIGMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a WIG point
WIGMouseLeaveLineOpacity

Line opacity when mouse leaving the element
WIGMouseLeaveLineStrokeColor

Stroke color when mouse leaving the element
WIGMouseLeaveLineStrokeWidth

Stroke width when mouse leaving the element
WIGMouseLeaveFillColor

Filling color when mouse leaving the element
WIGMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a WIG point
WIGMouseMoveLineOpacity

Line opacity when mouse moving in the element
WIGMouseMoveLineStrokeColor

Stroke color when mouse moving in the element
WIGMouseMoveLineStrokeWidth

Stroke width when mouse moving in the element
WIGMouseMoveFillColor

Filling color when mouse leaving the element
WIGMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a WIG point anymore
WIGMouseOutAnimationTime

Animation time when mouse moving out the element
WIGMouseOutLineOpacity

Line opacity when mouse moving out the element
WIGMouseOutLineStrokeColor

Stroke color when mouse moving out the element
WIGMouseOutLineStrokeWidth

Stroke width when mouse moving out the element
WIGMouseOutFillColor

Filling color when mouse moving out the element
WIGMouseUpDisplay

Default False, show/not the tooltip when mouse click up a WIG point
WIGMouseUpLineOpacity

Line opacity when mouse moving up the element
WIGMouseUpLineStrokeColor

Stroke color when mouse moving up the element
WIGMouseUpLineStrokeWidth

Stroke width when mouse moving up the element
WIGMouseUpFillColor

Filling color when mouse moving up the element
WIGMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a WIG point
WIGMouseOverLineOpacity

Line opacity when mouse moving over the element
WIGMouseOverLineStrokeColor

Stroke color when mouse moving over the element
WIGMouseOverLineStrokeWidth

Stroke width when mouse moving over the element
WIGMouseOverFillColor

Filling color when mouse moving over the element
WIGMouseOverTooltipsSetting

Default "style1"
WIGMouseOverTooltipsHtml

Default " "
WIGMouseOverTooltipsPosition

Default "absolute"
WIGMouseOverTooltipsBackgroundColor

Default "white"
WIGMouseOverTooltipsBorderStyle

Default "solid"
WIGMouseOverTooltipsBorderWidth

Default 0
WIGMouseOverTooltipsPadding

Default "3px"
WIGMouseOverTooltipsBorderRadius

Default "3px"
WIGMouseOverTooltipsOpacity

Default 0.8
SCATTERxlink

Default False, add/not xlink for SCATTER module
SCATTERMouseEvent

Default True, open/not open mouse event of SCATTER module
SCATTERMouseClickDisplay

Default False, show/not the tooltip when mouse click on a SCATTER point
SCATTERMouseClickColor

Color when mouse clicking the element
SCATTERMouseClickCircleSize

Circle size when mouse clicking the element
SCATTERMouseClickCircleOpacity

Circle opacity when mouse clicking the element
SCATTERMouseClickCircleStrokeColor

Circle stroke color when mouse clicking the element
SCATTERMouseClickCircleStrokeWidth

Circle stroke width when mouse clicking the element
SCATTERMouseClickTextFromData

Text column when mouse clicking the element
SCATTERMouseClickTextOpacity

Text opacity when mouse clicking the element
SCATTERMouseClickTextColor

Text color when mouse clicking the element
SCATTERMouseClickTextSize

Text size when mouse clicking the element
SCATTERMouseClickTextPostionX, SCATTERMouseClickTextPostionY

Text coordinates when mouse clicking the element
SCATTERMouseClickTextDrag

Whether text is draggable when clicing element
SCATTERMouseDownDisplay

Default False, show/not the tooltip when mouse click down a SCATTER point
SCATTERMouseDownColor

Color when mouse moving down the element
SCATTERMouseDownCircleSize

Circle size when mouse moving down the element
SCATTERMouseDownCircleOpacity

Circle opacity when mouse moving down the element
SCATTERMouseDownCircleStrokeColor

Circle stroke color when mouse moving down the element
SCATTERMouseDownCircleStrokeWidth

Circle stroke width when mouse moving down the element
SCATTERMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a SCATTER point
SCATTERMouseEnterColor

Color when mouse entering the element
SCATTERMouseEnterCircleSize

Circle size when mouse entering the element
SCATTERMouseEnterCircleOpacity

Circle opacity when mouse entering the element
SCATTERMouseEnterCircleStrokeColor

Circle stroke color when mouse entering the element
SCATTERMouseEnterCircleStrokeWidth

Circle stroke width when mouse entering the element
SCATTERMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a SCATTER point
SCATTERMouseLeaveColor

Color when mouse leaving the element
SCATTERMouseLeaveCircleSize

Circle size when mouse leaving the element
SCATTERMouseLeaveCircleOpacity

Circle opacity when mouse leaving the element
SCATTERMouseLeaveCircleStrokeColor

Circle stroke color when mouse leaving the element
SCATTERMouseLeaveCircleStrokeWidth

Circle stroke width when mouse leaving the element
SCATTERMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a SCATTER point
SCATTERMouseMoveColor

Color when mouse moving in the element
SCATTERMouseMoveCircleSize

Circle size when mouse moving in the element
SCATTERMouseMoveCircleOpacity

Circle opacity when mouse moving in the element
SCATTERMouseMoveCircleStrokeColor

Circle stroke color when mouse moving in the element
SCATTERMouseMoveCircleStrokeWidth

Circle stroke width when mouse moving in the element
SCATTERMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a SCATTER point anymore
SCATTERMouseOutAnimationTime

Animation time when mouse moving out the element
SCATTERMouseOutColor

Color when mouse moving out the element
SCATTERMouseOutCircleSize

Circle size when mouse moving out the element
SCATTERMouseOutCircleOpacity

Circle opacity when mouse moving out the element
SCATTERMouseOutCircleStrokeColor

Circle stroke color when mouse moving out the element
SCATTERMouseOutCircleStrokeWidth

Circle stroke width when mouse moving out the element
SCATTERMouseUpDisplay

Default False, show/not the tooltip when mouse click up a SCATTER point
SCATTERMouseUpColor

Color when mouse moving up the element
SCATTERMouseUpCircleSize

Circle size when mouse moving up the element
SCATTERMouseUpCircleOpacity

Circle opacity when mouse moving up the element
SCATTERMouseUpCircleStrokeColor

Circle stroke color when mouse moving up the element
SCATTERMouseUpCircleStrokeWidth

Circle stroke width when mouse moving up the element
SCATTERMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a SCATTER point
SCATTERMouseOverColor

Color when mouse moving over the element
SCATTERMouseOverCircleSize

Circle size when mouse moving over the element
SCATTERMouseOverCircleOpacity

Circle opacity when mouse moving over the element
SCATTERMouseOverCircleStrokeColor

Circle stroke color when mouse moving over the element
SCATTERMouseOverCircleStrokeWidth

Circle stroke width when mouse moving over the element
SCATTERMouseOverTooltipsSetting

Default "style1"
SCATTERMouseOverTooltipsHtml

Default " "
SCATTERMouseOverTooltipsPosition

Default "absolute"
SCATTERMouseOverTooltipsBackgroundColor

Default "white"
SCATTERMouseOverTooltipsBorderStyle

Default "solid"
SCATTERMouseOverTooltipsBorderWidth

Default 0
SCATTERMouseOverTooltipsPadding

Default "3px"
SCATTERMouseOverTooltipsBorderRadius

Default "3px"
SCATTERMouseOverTooltipsOpacity

Default 0.8
ARCxlink

Default False, add/not xlink for ARC module
ARCMouseEvent

Default True, open/not open mouse event of ARC module
ARCMouseClickDisplay

Default False, show/not the tooltip when mouse click on a ARC point
ARCMouseClickColor

Color when mouse clicking the element
ARCMouseClickArcOpacity

Arc opacity when mouse clicking the element
ARCMouseClickArcStrokeColor

Arc stroke color when mouse clicking the element
ARCMouseClickArcStrokeWidth

Arc stroke width when mouse clicking the element
ARCMouseClickTextFromData

Text column when mouse clicking the element
ARCMouseClickTextOpacity

Text opacity when mouse clicking the element
ARCMouseClickTextColor

Text color when mouse clicking the element
ARCMouseClickTextSize

Text size when mouse clicking the element
ARCMouseClickTextPostionX, ARCMouseClickTextPostionY

Text coordinates when mouse clicking the element
ARCMouseClickTextDrag

Whether text is draggable when mouse clicking the element
ARCMouseDownDisplay

Default False, show/not the tooltip when mouse click down a ARC point
ARCMouseDownColor

Color when mouse moving down the element
ARCMouseDownArcOpacity

Arc opacity when mouse moving down the element
ARCMouseDownArcStrokeColor

Arc stroke color when mouse moving down the element
ARCMouseDownArcStrokeWidth

Arc stroke width when mouse moving down the element
ARCMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a ARC point
ARCMouseEnterColor

Color when mouse entering the element
ARCMouseEnterArcOpacity

Arc opacity when mouse entering the element
ARCMouseEnterArcStrokeColor

Arc stroke color when mouse entering the element
ARCMouseEnterArcStrokeWidth

Arc stroke width when mouse entering the element
ARCMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a ARC point
ARCMouseLeaveColor

Color when mouse leaving the element
ARCMouseLeaveArcOpacity

Arc opacity when mouse leaving the element
ARCMouseLeaveArcStrokeColor

Arc stroke color when mouse leaving the element
ARCMouseLeaveArcStrokeWidth

Arc stroke width when mouse leaving the element
ARCMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a ARC point
ARCMouseMoveColor

Color when mouse moving in the element
ARCMouseMoveArcOpacity

Arc opacity when mouse moving in the element
ARCMouseMoveArcStrokeColor

Arc stroke color when mouse moving in the element
ARCMouseMoveArcStrokeWidth

Arc stroke width when mouse moving in the element
ARCMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a ARC point anymore
ARCMouseOutAnimationTime

Animation time when mouse moving out the element
ARCMouseOutColor

Color when mouse moving out the element
ARCMouseOutArcOpacity

Arc opacity when mouse moving out the element
ARCMouseOutArcStrokeColor

Arc stroke color when mouse moving out the element
ARCMouseOutArcStrokeWidth

Arc stroke width when mouse moving out the element
ARCMouseUpDisplay

Default False, show/not the tooltip when mouse click up a ARC point
ARCMouseUpColor

Color when mouse moving up the element
ARCMouseUpArcOpacity

Arc opacity when mouse moving up the element
ARCMouseUpArcStrokeColor

Arc stroke color when mouse moving up the element
ARCMouseUpArcStrokeWidth

Arc stroke width when mouse moving up the element
ARCMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a ARC point
ARCMouseOverColor

Color when mouse moving over the element
ARCMouseOverArcOpacity

Arc opacity when mouse moving over the element
ARCMouseOverArcStrokeColor

Arc stroke color when mouse moving over the element
ARCMouseOverArcStrokeWidth

Arc stroke width when mouse moving over the element
ARCMouseOverTooltipsSetting

Default "style1"
ARCMouseOverTooltipsHtml

Default " "
ARCMouseOverTooltipsPosition

Default "absolute"
ARCMouseOverTooltipsBackgroundColor

Default "white"
ARCMouseOverTooltipsBorderStyle

Default "solid"
ARCMouseOverTooltipsBorderWidth

Default 0
ARCMouseOverTooltipsPadding

Default "3px"
ARCMouseOverTooltipsBorderRadius

Default "3px"
ARCMouseOverTooltipsOpacity

Default 0.8
GENExlink

Default False, add/not xlink for GENE module
GENEMouseEvent

Default True, open/not open mouse event of GENE module
GENEMouseClickDisplay

Default False, show/not the tooltip when mouse click on a GENE point
GENEMouseClickColor

Color when mouse clicking the element
GENEMouseClickArcOpacity

Arc opacity when mouse clicking the element
GENEMouseClickArcStrokeColor

Arc stroke color when mouse clicking the element
GENEMouseClickArcStrokeWidth

Arc stroke width when mouse clicking the element
GENEMouseClickTextFromData

Text column when mouse clicking the element
GENEMouseClickTextOpacity

Text opacity when mouse clicking the element
GENEMouseClickTextColor

Text color when mouse clicking the element
GENEMouseClickTextSize

Text size when mouse clicking the element
GENEMouseClickTextPostionX, GENEMouseClickTextPostionY

Text coordinates when mouse clicking the element
GENEMouseClickTextDrag

Whether text is draggable when mouse clicking the element
GENEMouseDownDisplay

Default False, show/not the tooltip when mouse click down a GENE point
GENEMouseDownColor

Color when mouse moving down the element
GENEMouseDownArcOpacity

Arc opacity when mouse moving down the element
GENEMouseDownArcStrokeColor

Arc stroke color when mouse moving down the element
GENEMouseDownArcStrokeWidth

Arc stroke width when mouse moving down the element
GENEMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a GENE point
GENEMouseEnterColor

Color when mouse entering the element
GENEMouseEnterArcOpacity

Arc opacity when mouse entering the element
GENEMouseEnterArcStrokeColor

Arc stroke color when mouse entering the element
GENEMouseEnterArcStrokeWidth

Arc stroke width when mouse entering the element
GENEMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a GENE point
GENEMouseLeaveColor

Color when mouse leaving the element
GENEMouseLeaveArcOpacity

Arc opacity when mouse leaving the element
GENEMouseLeaveArcStrokeColor

Arc stroke color when mouse leaving the element
GENEMouseLeaveArcStrokeWidth

Arc stroke width when mouse leaving the element
GENEMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a GENE point
GENEMouseMoveColor

Color when mouse moving in the element
GENEMouseMoveArcOpacity

Arc opacity when mouse moving in the element
GENEMouseMoveArcStrokeColor

Arc stroke color when mouse moving in the element
GENEMouseMoveArcStrokeWidth

Arc stroke width when mouse moving in the element
GENEMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a GENE point anymore
GENEMouseOutAnimationTime

Animation time when mouse moving out the element
GENEMouseOutColor

Color when mouse moving out the element
GENEMouseOutArcOpacity

Arc opacity when mouse moving out the element
GENEMouseOutArcStrokeColor

Arc stroke color when mouse moving out the element
GENEMouseOutArcStrokeWidth

Arc stroke width when mouse moving out the element
GENEMouseUpDisplay

Default False, show/not the tooltip when mouse click up a GENE point
GENEMouseUpColor

Color when mouse moving up the element
GENEMouseUpArcOpacity

Arc opacity when mouse moving up the element
GENEMouseUpArcStrokeColor

Arc stroke color when mouse moving up the element
GENEMouseUpArcStrokeWidth

Arc stroke width when mouse moving up the element
GENEMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a GENE point
GENEMouseOverColor

Color when mouse moving over the element
GENEMouseOverArcOpacity

Arc opacity when mouse moving over the element
GENEMouseOverArcStrokeColor

Arc stroke color when mouse moving over the element
GENEMouseOverArcStrokeWidth

Arc stroke width when mouse moving over the element
GENEMouseOverTooltipsSetting

Default "style1"
GENEMouseOverTooltipsHtml

Default " "
GENEMouseOverTooltipsPosition

Default "absolute"
GENEMouseOverTooltipsBackgroundColor

Default "white"
GENEMouseOverTooltipsBorderStyle

Default "solid"
GENEMouseOverTooltipsBorderWidth

Default 0
GENEMouseOverTooltipsPadding

Default "3px"
GENEMouseOverTooltipsBorderRadius

Default "3px"
GENEMouseOverTooltipsOpacity

Default 0.8
LOLLIPOPxlink

Default False, add/not xlink for LOLLIPOP module
LOLLIPOPMouseEvent

Default True, open/not open mouse event of LOLLIPOP module
LOLLIPOPMouseClickDisplay

Default False, show/not the tooltip when mouse click on a LOLLIPOP point
LOLLIPOPMouseClickColor

Color when mouse clicking
LOLLIPOPMouseClickCircleSize

Circle size when mouse clicking the element
LOLLIPOPMouseClickCircleOpacity

Circle opacity when mouse clicking the element
LOLLIPOPMouseClickCircleStrokeColor

Circle stroke color when mouse clicking the element
LOLLIPOPMouseClickCircleStrokeWidth

Circle stroke width when mouse clicking the element
LOLLIPOPMouseClickTextFromData

Text column when mouse clicking the element
LOLLIPOPMouseClickTextOpacity

Text opacity when mouse clicking the element
LOLLIPOPMouseClickTextColor

Text color when mouse clicking the element
LOLLIPOPMouseClickTextSize

Text size when mouse clicking the element
LOLLIPOPMouseClickTextPostionX, LOLLIPOPMouseClickTextPostionY

Text coordinates when mouse clicking the element
LOLLIPOPMouseClickTextDrag

Whether text is draggable when mouse clicking the element
LOLLIPOPMouseDownDisplay

Default False, show/not the tooltip when mouse click down a LOLLIPOP point
LOLLIPOPMouseDownColor

Color when mouse moving down the element
LOLLIPOPMouseDownCircleSize

Circle size when mouse moving down the element
LOLLIPOPMouseDownCircleOpacity

Circle opacity when mouse moving down the element
LOLLIPOPMouseDownCircleStrokeColor

Circle stroke color when mouse moving down the element
LOLLIPOPMouseDownCircleStrokeWidth

Circle stroke width when mouse moving down the element
LOLLIPOPMouseEnterDisplay

Default False, show/not the tooltip when mouse mover over a LOLLIPOP point
LOLLIPOPMouseEnterColor

Color when mouse entering the element
LOLLIPOPMouseEnterCircleSize

Circle size when mouse entering the element
LOLLIPOPMouseEnterCircleOpacity

Circle opacity when mouse entering the element
LOLLIPOPMouseEnterCircleStrokeColor

Circle stroke color when mouse entering the element
LOLLIPOPMouseEnterCircleStrokeWidth

Circle stroke width when mouse entering the element
LOLLIPOPMouseLeaveDisplay

Default False, show/not the tooltip when mouse mover leave a LOLLIPOP point
LOLLIPOPMouseLeaveColor

Color when mouse leaving the element
LOLLIPOPMouseLeaveCircleSize

Circle size when mouse leaving the element
LOLLIPOPMouseLeaveCircleOpacity

Circle opacity when mouse leaving the element
LOLLIPOPMouseLeaveCircleStrokeColor

Circle stroke color when mouse leaving the element
LOLLIPOPMouseLeaveCircleStrokeWidth

Circle stroke width when mouse leaving the element
LOLLIPOPMouseMoveDisplay

Default False, show/not the tooltip when mouse move into a LOLLIPOP point
LOLLIPOPMouseMoveColor

Color when mouse moving in the element
LOLLIPOPMouseMoveCircleSize

Circle size when mouse moving in the element
LOLLIPOPMouseMoveCircleOpacity

Circle opacity when mouse moving in the element
LOLLIPOPMouseMoveCircleStrokeColor

Circle stroke color when mouse moving in the element
LOLLIPOPMouseMoveCircleStrokeWidth

Circle stroke width when mouse moving in the element
LOLLIPOPMouseOutDisplay

Defalut False, hide/not tooltip when mouse is not hovering a LOLLIPOP point anymore
LOLLIPOPMouseOutAnimationTime

Animation time when mouse moving out the element
LOLLIPOPMouseOutColor

Color when mouse moving out the element
LOLLIPOPMouseOutCircleSize

Circle size when mouse moving out the element
LOLLIPOPMouseOutCircleOpacity

Circle opacity when mouse moving out the element
LOLLIPOPMouseOutCircleStrokeColor

Circle stroke color when mouse moving out the element
LOLLIPOPMouseOutCircleStrokeWidth

Circle stroke width when mouse moving out the element
LOLLIPOPMouseUpDisplay

Default False, show/not the tooltip when mouse click up a LOLLIPOP point
LOLLIPOPMouseUpColor

Color when mouse moving up the element
LOLLIPOPMouseUpCircleSize

Circle size when mouse moving up the element
LOLLIPOPMouseUpCircleOpacity

Circle opacity when mouse moving up the element
LOLLIPOPMouseUpCircleStrokeColor

Circle stroke color when mouse moving up the element
LOLLIPOPMouseUpCircleStrokeWidth

Circle stroke width when mouse moving up the element
LOLLIPOPMouseOverDisplay

Default False, show/not the tooltip when mouse hover on a LOLLIPOP point
LOLLIPOPMouseOverColor

Color when mouse moving over the element
LOLLIPOPMouseOverCircleSize

Circle size when mouse moving over the element
LOLLIPOPMouseOverCircleOpacity

Circle opacity when mouse moving over the element
LOLLIPOPMouseOverCircleStrokeColor

Circle stroke color when mouse moving over the element
LOLLIPOPMouseOverCircleStrokeWidth

Circle stroke width when mouse moving over the element
LOLLIPOPMouseOverTooltipsSetting

Default "style1"
LOLLIPOPMouseOverTooltipsHtml

Default " "
LOLLIPOPMouseOverTooltipsPosition

Default "absolute"
LOLLIPOPMouseOverTooltipsBackgroundColor

Default "white"
LOLLIPOPMouseOverTooltipsBorderStyle

Default "solid"
LOLLIPOPMouseOverTooltipsBorderWidth

Default 0
LOLLIPOPMouseOverTooltipsPadding

Default "3px"
LOLLIPOPMouseOverTooltipsBorderRadius

Default "3px"
LOLLIPOPMouseOverTooltipsOpacity

Default 0.8
elementId

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

Ignored

Value

The main figure for interacCircos with all tracks

Examples

Circos(genome = "hg19")

ARC module

Description

Create the CNV plot without value, Gene domain, Chromosome band

Usage

CircosArc(
  modulename,
  compareGroup = 1,
  outerRadius = 150,
  innerRadius = 130,
  opacity = 1,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
innerRadius, outerRadius

Where the module should begin and end
opacity

The opacity for arc
animationDisplay

Whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of arc with details including chr, start, end, color, des, link and html. Details can be found on document
...

Ignored

Value

The module tracks for arc modules

Examples

arcData<-arcExample
Circos(CircosArc('Arc01', outerRadius = 212, innerRadius = 224, data=arcData),
 genome=list("EGFR"=1211),outerRadius = 220,genomeFillColor = c("grey"))

AUXILIARYLINE module

Description

A auxiliary line for better explaination of the visualization

Usage

CircosAuxLine(
  modulename,
  startX = 20,
  startY = 20,
  endX = 120,
  endY = 120,
  color = "red",
  width = 0.5,
  type = "straight",
  controlPointX = 0,
  controlPointY = 0,
  lineType = "solid",
  dashArray = 3,
  marker = TRUE,
  markerType = "circle",
  markerColor = "blue",
  markerHeight = 5,
  markerWidth = 5,
  markerPosition = 2,
  animationDisplay = FALSE,
  animationTime = 50,
  animationDelay = 1000,
  animationType = "linear",
  ...
)

Arguments

modulename

The name of the new module
startX, startY

Start coordinates for auxiliary line
endX, endY

End coordinates for auxiliary line
color

Color for auxiliary line
width

Width for auxiliary line
type

Type for auxiliary line, could be straight/curve/broken
controlPointX, controlPointY

The middle point coordinates for curve and broken
lineType

Line type, could be solid/dot
dashArray

The dash gap width
marker

Whether display a marker on the end of line
markerType

Type of marker, could be circle/square/arrow/stub
markerColor, markerHeight, markerWidth

Color, Height and Width for marker
markerPosition

1 means start, 2 means end, 3 means both
animationDisplay

whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
...

Ignored

Value

The module tracks for auxliary line modules

Examples

Circos(CircosAuxLine('AuxLine01'))

BACKGROUND module

Description

Background for better display of other modules

Usage

CircosBackground(
  modulename,
  compareGroup = 1,
  fillColors = "#EEEEFF",
  borderColors = "#000000",
  axisShow = FALSE,
  axisColor = "#000",
  axisOpacity = 0.5,
  axisNum = 4,
  axisWidth = 0.3,
  maxRadius = 190,
  minRadius = 105,
  borderSize = 0.3,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
fillColors

The filling color of the module
borderColors

The border color of the module
axisShow

Whether show a axis or not
axisWidth, axisColor, axisOpacity, axisNum

The color, opacity value and number of line for axis
minRadius, maxRadius

The outer and inner ring range of module
borderSize

The thickness of the border
animationDisplay

Whether display animation or not
animationTime, animationDelay, animationType

The time, delay and display type for animation
...

Ignored

Value

The module tracks for background modules.

Examples

Circos(CircosBackground('bg01', fillColors="#FFEEEE", borderSize = 1))

BUBBLE module

Description

Create a bubble plot

Usage

CircosBubble(
  modulename,
  compareGroup = 1,
  maxRadius = 200,
  minRadius = 50,
  blockStroke = TRUE,
  blockStrokeColor = "black",
  blockStrokeWidth = 1,
  blockFill = FALSE,
  blockFillColor = "white",
  bubbleMaxSize = 5,
  bubbleMinSize = 2,
  minColor = "red",
  maxColor = "green",
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  totalLayer = 1,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

The outer and inner ring range of module
blockStroke

Whether display the stroke between each bubble block
blockStrokeColor

Stroke color for block
blockStrokeWidth

Stroke width for block
blockFill

Whether fill a block or not
blockFillColor

The color for filling the block
bubbleMaxSize

The max size for bubble
bubbleMinSize

The min size for bubble
minColor

The color the bubble of min value
maxColor

The color the bubble of max value
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
totalLayer

The color and width for stroke
animationDisplay

Whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of value in bubble plot with details including chr, start, end, value, name, layer, color and html. Details can be found on document
...

Ignored

Value

The module tracks for bubble modules

Examples

bubbleData<-bubbleExample
Circos(CircosBubble('Bubble01', maxRadius = 230, minRadius = 170, data=bubbleData, 
blockStroke = TRUE, bubbleMaxSize =10, bubbleMinSize = 2, maxColor = "red", minColor = "yellow",
totalLayer =3, animationDisplay = TRUE, animationType="linear"),
genome = list("2L"=23011544,"2R"=21146708,"3L"=24543557,"3R"= 27905053,"X"=22422827,"4"=1351857),
BUBBLEMouseOverDisplay =TRUE,innerRadius = 236)

CHORD module of NG-Circos

Description

Create a chord module using a data matrix

Usage

CircosChord(
  modulename,
  innerRadius = 237,
  outerRadius = 238,
  fillOpacity = 0.67,
  fillStrokeWidth = 1,
  padding = 0.06,
  autoFillColor = TRUE,
  fillColor = c("#B8B8B8"),
  fillStrokeColor = c("black"),
  outerARC = TRUE,
  outerARCAutoColor = TRUE,
  outerARCColor = c("red"),
  outerARCStrokeColor = c("black"),
  outerARCText = TRUE,
  data,
  ...
)

Arguments

modulename

The name of the new module
innerRadius

The inner radius for chord circle
outerRadius

The outer radius for chord circle
fillOpacity

The opacity for filling color
fillStrokeWidth

The stroke width for chord
padding

The pad of chord
autoFillColor

Whether auto assign color for chord
fillColor

If not, manually assign color for chord
fillStrokeColor

The color for stroke
outerARC

Whether display outer arc
outerARCAutoColor

If true, whether auto assign color for arc
outerARCColor

The manullay assigned color for arc
outerARCStrokeColor

The stroke color for arc
outerARCText

Whether display text for arc or not
data

A matrix-list of chord value with relationship details
...

Ignored

Value

The module tracks for chord modules of NG-Circos

Examples

chordData<-chordExample
Circos(CircosChord('CHORD', data = chordData,innerRadius= 210,outerRadius= 211,fillOpacity=0.67,
strokeColor="black",strokeWidth= "1px",outerARCText=FALSE),genome=list("C.CK" = 189.51,"C.NPK"=188,
"GC.CK"=186.11, "GC.NPK"=191.51,"Alphaproteobacteria"=70.16,"Betaproteobacteria"=23.51,
"Gammaproteobacteria"=25.51, "Deltaproteobacteria"=23.28,"Acidobacteria"=53.62,
"Actinobacteria"=72.33, "Bacteroidetes"=22.41, "Chloroflexi"=15.08,"Firmicutes"=10.72,
"Gemmatimonadetes"=26.37, "Planctomycetes"=19.26,"Thaumarchaeota"=6.15, "Verrucomicrobia"=8.3,
"Ascomycota"=159.41, "Basidiomycota"=79.73,"Zygomycota"=139.29 ),outerRadius = 217, 
genomeLabelDisplay = FALSE)

CHORD module of circosJS

Description

Create a chord module using a data path. chord.p meaens chord plot based on path

Usage

CircosChord.p(
  modulename,
  radius = 216,
  opacity = 0.67,
  color = "#B8B8B8",
  data,
  ...
)

Arguments

modulename

The name of the new module
radius

The radius for chord circle
opacity

The opacity for chord
color

The color for chord
data

A list of chord value with relationship details, details could be found on chord.pExample
...

Ignored

Value

The module tracks for chord modules of circosJS

Examples

chord.pData<-chord.pExample
Circos()

CNV module

Description

Create a copy number variance module

Usage

CircosCnv(
  modulename,
  compareGroup = 1,
  maxRadius = 200,
  minRadius = 190,
  width = 10,
  color = "#CAE1FF",
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  strokeColor = "black",
  strokeWidth = 1,
  opacity = 1,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 50,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

The outer and inner ring range of module
width

Width for CNV module
color

Color for CNV module
ValueAxisManualScale

Whether manually control the scale of value or not
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
strokeColor, strokeWidth

The color and width for stroke
opacity

The opacity for module
animationDisplay

Whether display animationn
animationTime, animationDelay, animationType

The time, delay and display type for animationn
data

A list of CNV with details including start, end, value, link, color and html. Details can be found on document
...

Ignored

Value

The module tracks for cnv modules

Examples

cnvData<-cnvExample
Circos(CircosCnv('Cnv01',maxRadius =175, minRadius =116, data =cnvData,width=2,color = "#4876FF")+
CircosBackground("bg01",minRadius = 116,maxRadius = 175,fillColors = "#F2F2F2",axisShow = TRUE),
CNVMouseOverDisplay = TRUE)

GENE module

Description

Create a number of genes with different functional region

Usage

CircosGene(
  modulename,
  compareGroup = 1,
  outerRadius = 180,
  innerRadius = 150,
  pathColor = "black",
  pathWidth = 1,
  arrow = TRUE,
  arrowGap = 2,
  arrowColor = "blue",
  arrowSize = 5,
  cdsColor = "#1e77b3",
  cdsStrokeColor = "black",
  cdsStrokeWidth = 1,
  utrWidth = -5,
  utrColor = "blue",
  utrStrokeColor = "blue",
  utrStrokeWidth = 1,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
outerRadius, innerRadius

Where the module should begin and end
pathColor

The color for path between gene elements
pathWidth

The width for path between gene elements
arrow

Whether display arrows on path
arrowGap, arrowColor, arrowSize

The gap, color and size for arrow
cdsColor, cdsStrokeColor, cdsStrokeWidth

The color, stroke color and stroke width for coding
utrWidth, utrColor, utrStrokeColor, utrStrokeWidth

The max size for bubble
animationDisplay

Whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of gene with details including chr, strand, start, end, type, name, link and html. Details can be found on document
...

Ignored

Value

The module tracks for gene modules

Examples

geneData<-geneExample
Circos(CircosGene('Gene01', outerRadius = 195, innerRadius = 180, data=geneData,arrowGap = 10,
 arrowColor = "black",arrowSize = "12px",cdsColor = "#1e77b3",cdsStrokeColor = "#1e77b3",
 cdsStrokeWidth= 5, utrWidth= -2,utrColor= "#fe7f0e",utrStrokeColor= "#fe7f0e",
 animationDisplay = TRUE),genome =list("EGFR"=1000), outerRadius = 220)

HEATMAP module

Description

Create a heatmap plot

Usage

CircosHeatmap(
  modulename,
  compareGroup = 1,
  maxRadius = 180,
  minRadius = 100,
  minColor = "red",
  maxColor = "green",
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  totalLayer = 1,
  animationDisplay = FALSE,
  animationDirection = "O2I",
  animationColorDirection = "L2C",
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

Where the module should begin and end
minColor

The color for heatmap of min value
maxColor

The color for heatmap of max value
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
totalLayer

The color and width for stroke
animationDisplay

Whether display animation
animationDirection

The direction for animation. O2I: from outside to inside, I2O: from inside to outside
animationColorDirection

The color changing in animation. L2C: lowest to customized, H2C: highest to customized, the customized color should be defined in data
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of value in heatmap plot with details including chr, start, end, value, name, layer and html. Details can be found on document
...

Ignored

Value

The module tracks for heatmap modules.

Examples

heatmapData<-heatmapExample
Circos(CircosHeatmap('Heatmap01', maxRadius= 180, minRadius = 100, data=heatmapData,totalLayer = 3),
genome = list("2L"=23011544,"2R"=21146708,"3L"=24543557,"3R"=27905053,"4"=1351857,"X"=22422827),
HEATMAPMouseEvent = TRUE,HEATMAPMouseOverDisplay = TRUE)

HISTOGRAM module

Description

Create a multi-layer histogram plot

Usage

CircosHistogram(
  modulename,
  compareGroup = 1,
  maxRadius = 108,
  minRadius = 95,
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  fillColor = "red",
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

Where the module should begin and end
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
fillColor

The color for histgram
animationDisplay

Whether display animation
animationTime, animationDelay

The time and delay for animation
data

A list of value with details including chr, start, end, name, link, value and html. Details can be found on document
...

Ignored

Value

The module tracks for histogram modules

Examples

histogramData<-histogramExample
Circos(CircosHistogram('HISTOGRAM01', data = histogramData,fillColor= "#ff7f0e",maxRadius = 210,
minRadius = 175),genome=list("2L"=23011544,"2R"=21146708,"3L"=24543557,"3R"= 27905053,
"X"=22422827,"4"=1351857),
outerRadius = 220)

LEGEND module

Description

Simple legend annotation displayed in the visualization

Usage

CircosLegend(
  modulename,
  x = 20,
  y = 20,
  title = "legend",
  size = 6,
  weight = "normal",
  GapBetweenGraphicText = 5,
  GapBetweenLines = 20,
  data,
  ...
)

Arguments

modulename

The name of the new module
x, y

The coordinates if legend
title

The title for legend
size

Font size for title
weight

Font weight for title. Should be either "normal", "bold", "bolder" or "lighter"
GapBetweenGraphicText

Gap between icon and text in legend
GapBetweenLines

Gap between each two lines in legend
data

A list of legend with details including type, color, opacity, circleSize, rectSize, lineWidth, lineHeight, text, textSize and textWeight. Details can be found on document
...

Ignored

Value

The module tracks for legend modules.

Examples

legend1 <- list(type= "circle", color="#1E77B4",opacity="1.0",circleSize="8",text= "C.CK", 
textSize= "14",textWeight="normal")
legend2 <- list(type= "circle", color="#AEC7E8",opacity="1.0",circleSize="8",text= "C.NPK", 
textSize= "14",textWeight="normal")
Circos(CircosLegend('legend01', title = "legend",data=list(legend1,legend2),size = 20))

LINE module

Description

Create a multi-layer line plot

Usage

CircosLine(
  modulename,
  compareGroup = 1,
  maxRadius = 108,
  minRadius = 95,
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  color = "red",
  width = 2,
  type = "cardinal",
  animationDisplay = FALSE,
  animationDirection = "S2E",
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

Where the module should begin and end
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
color

Color for line
width

Width for line
type

Type for line, could be linear, cardinal, basis and monotone
animationDisplay

Whether display animation
animationDirection

The direction of animation, could be S2E(start to end) or E2S(end to start)
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of value with details including chr, pos, des, value and html. Details can be found on document
...

Ignored

Value

The module tracks for line modules

Examples

lineData<-lineExample
Circos(CircosLine('LINE01', data = lineData,maxRadius=200,minRadius=150,color= "#ff0031")+
CircosBackground('BG01',minRadius = 205,maxRadius = 150))

LINK module

Description

Create a link of two specific region in genome

Usage

CircosLink(
  modulename,
  compareGroup = 1,
  radius = 108,
  fillColor = "red",
  width = 3,
  type = "Q",
  displayLinkAxis = TRUE,
  axisColor = "#B8B8B8",
  axisWidth = 0.5,
  axisPad = 3,
  displayLinkLabel = TRUE,
  labelColor = "red",
  labelSize = 13,
  labelPad = 8,
  animationDisplay = FALSE,
  animationDirection = "1to2",
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of thic module in compare module
radius

Radius of link circle
fillColor

Color for link
width

Width for link
type

Type of link, could be Q/S/T
displayLinkAxis

Whether display axis for link or not
axisColor

The color for axis
axisWidth

The width for axis
axisPad

The pad for axis
displayLinkLabel

Whether display label for link or not
labelColor

The color for label
labelSize

The size for label
labelPad

The pad for label
animationDisplay

Whether display animation
animationDirection

The direction of link animation, could be 1to2 or 2to1
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of link with details including g1chr, g1start, g1end, g2chr, g2start, g2end, g1name, g2name, fusion, link and html. Details can be found on document
...

Ignored

Value

The module tracks for link modules

Examples

linkData<-linkExample
Circos(CircosLink('LINK', data = linkData,LinkRadius= 140,fillColor= "#9e9ac6",width= 2,
axisPad= 3,labelPad=8,animationDisplay=TRUE,animationDirection="1to2", animationType= "linear" ))

LOLLIPOP module

Description

Create a lollipop plot

Usage

CircosLollipop(
  modulename,
  compareGroup = 1,
  fillColor = "#9400D3",
  secondColor = "#FFFFFF",
  pointType = "circle",
  circleSize = 2,
  diamondWidth = 10,
  diamondHeight = 5,
  rectWidth = 2,
  rectHeight = 2,
  stroke = TRUE,
  strokeColor = "#000000",
  strokeWidth = 0.5,
  lineAutoHeight = TRUE,
  lineAutoMaximumHeightZoomRate = 1,
  lineHeightRate = 0.75,
  lineWidth = 2,
  lineColor = "#000000",
  realStart = 0,
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
fillColor

Filling color for lollipop
secondColor

Second filling color for heterogeneous lollipop
pointType

The type for lollipop, could be circle, rect and diamond
circleSize

If circle, the size for lollipop
diamondWidth, diamondHeight

If diamond, the width and height for lollipop
rectWidth, rectHeight

If rect, the width and height for lollipop
stroke

Whether display the stroke for lollipop
strokeColor, strokeWidth

The color and width for stroke
lineAutoHeight

Whether auto assign the height for each lollipop
lineAutoMaximumHeightZoomRate

If auto assign, the zoom rate for each lollipop
lineHeightRate

If manually assign, the rate of lollipop compared to real value
lineWidth, lineColor

The width and color for the line of lollipop
realStart

The real start position for data in genome
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
animationDisplay

Whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of lollipop value with details including protein, chr, pos, strand, CancerTypeNumber, color, link, Consequence, AA_pos, AA_change, type, link and html. Details can be found on document
...

Ignored

Value

The module tracks for lollipop modules.

Examples

lollipopData<-lollipopExample
arcData<-arcExample
Circos(CircosLollipop('Lollipop01', data=lollipopData, fillColor="#9400D3",
circleSize= 6, strokeColor= "#999999", strokeWidth= "1px", animationDisplay=TRUE, lineWidth= 2,
realStart= 101219350)+CircosArc('Arc01', outerRadius = 212, innerRadius = 224, data=arcData),
 genome=list("EGFR"=1211),outerRadius = 220,genomeFillColor = c("grey"))

Create a list of modules

Description

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

Usage

CircosModuleList()

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

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

Arguments

x

The moduleList on which other modules should be added or removed
...

The modules to add (as moduleLists) or to remove (as module names)

Value

The list of all tracks of modules.

SCATTER module

Description

Create a point plot

Usage

CircosScatter(
  modulename,
  compareGroup = 1,
  radius = 140,
  innerCircleSize = 1,
  outerCircleSize = 5,
  innerCircleColor = "#F26223",
  outerCircleColor = "#F26223",
  innerPointType = "circle",
  outerPointType = "circle",
  innerrectWidth = 2,
  innerrectHeight = 2,
  outerrectWidth = 2,
  outerrectHeight = 2,
  outerCircleOpacity = 1,
  random_data = 0,
  animationDisplay = FALSE,
  animationInitialPositionX = 0,
  animationInitialPositionY = 0,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
radius

Radius of scatter circle
innerCircleSize, outerCircleSize

If circle, inner and outer circle size
innerCircleColor, outerCircleColor

If circle, inner and outer circle color
innerPointType, outerPointType

The type for inner and outer point, could be circle or rect
innerrectWidth, innerrectHeight

If rect, inner width and height
outerrectWidth, outerrectHeight

If rect, inner width and height
outerCircleOpacity

If circle, the opacity for outer circle
random_data

Scatter position fluctuation
animationDisplay

Whether display animation
animationInitialPositionX, animationInitialPositionY

The initial coordinates for animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of value with details including chr, start, end, name, des, link and html. Details can be found on document
...

Ignored

Value

The module tracks for scatter modules

Examples

scatterData<-scatterExample
Circos(CircosScatter('SCATTER01', data = scatterData,radius=180,innerCircleColor= "#3d6390",
outerCircleColor= "#99cafe",random_data= 40))

SNP module

Description

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

Usage

CircosSnp(
  modulename,
  compareGroup = 1,
  minRadius = 153,
  maxRadius = 205,
  fillColorType = "specific",
  fillColor = "#9400D3",
  fillr2Color = c("13#ff0031", "#ff0031", "#ff0031", "#ff0031", "#ff0031"),
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  pointType = "circle",
  circleSize = 2,
  rectWidth = 2,
  rectHeight = 2,
  animationDisplay = FALSE,
  animationInitialPositionX = 0,
  animationInitialPositionY = 0,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

Where the module should begin and end
fillColorType

The type of filling color, could be either specific or r2(means based on r2)
fillColor

If specific, the color for SNP filling
fillr2Color

If r2, the color for SNP filling
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
pointType

The type of SNP point, could be circle or rect
circleSize

If circle, the size for SNP circle
rectWidth

If rect, the width for SNP rect
rectHeight

If rect, the height for SNP rect
animationDisplay

Whether display animation
animationInitialPositionX, animationInitialPositionY

The initial position coordinates for animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of SNP value with details including chr, pos, value, des, color, r2value, link, index, image and html. Details can be found on document
...

Ignored

Value

The module tracks for snp modules

Examples

snpData<-snpExample
Circos(CircosSnp('SNP01', minRadius =150, maxRadius = 190, data = snpExample,fillColor= "#9ACD32",
   circleSize= 2, SNPAnimationDisplay=TRUE,SNPAnimationTime= 2000,SNPAnimationDelay= 0,
    SNPAnimationType= "linear") + CircosBackground('BG01',minRadius = 145, maxRadius = 200))

Text module

Description

Text for better explaination of other modules

Usage

CircosText(
  modulename,
  text,
  x = 0,
  y = 0,
  size = "1.2em",
  weight = "bold",
  opacity = 1,
  color = "#000000",
  rotateRate = 0,
  animationDisplay = FALSE,
  animationInitialSize = 20,
  animationInitialWeight = "bold",
  animationInitialColor = "black",
  animationInitialOpacity = 1,
  animationInitialPositionX = 0,
  animationInitialPositionY = 0,
  animationInitialRotate = 0,
  animationDelay = 50,
  animationTime = 1000,
  animationType = "linear",
  ...
)

Arguments

modulename

The name of the new module
text

The details of text
x, y

The coordinates of the text
size

Font size
weight

Font weight. Should be either "normal", "bold", "bolder" or "lighter"
opacity

Font opacity
color

Font color
rotateRate

ratate rate for text
animationDisplay

Whether display animation or not
animationInitialSize

Initial text size in animation
animationInitialWeight

Initial text weight in animation
animationInitialColor

Initial text color in animation
animationInitialOpacity

Initial text opacity in animation
animationInitialPositionX, animationInitialPositionY

Initial text coordinates in animation(The parameter x,y will become the final position for text if animation displayed)
animationInitialRotate

Initial rotate rate in animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
...

Ignored

Value

The module tracks for text modules.

Examples

Circos(CircosText('text01', 'Annotation', color = '#DD2222', x = -40))

WIG module

Description

Create a multi-layer line plot

Usage

CircosWig(
  modulename,
  compareGroup = 1,
  maxRadius = 108,
  minRadius = 95,
  direction = "out",
  ValueAxisManualScale = FALSE,
  ValueAxisMaxScale = 10,
  ValueAxisMinScale = 0,
  color = "red",
  opacity = 1,
  strokeColor = "black",
  strokeWidth = 1,
  strokeType = "cardinal",
  animationDisplay = FALSE,
  animationTime = 2000,
  animationDelay = 20,
  animationType = "bounce",
  data,
  ...
)

Arguments

modulename

The name of the new module
compareGroup

The group number of this module in compare module
maxRadius, minRadius

Where the module should begin and end
direction

The direction of plot, either inside or outside
ValueAxisManualScale

Whether manually control the scale of value
ValueAxisMaxScale, ValueAxisMinScale

The max and min scale value for manually control
color

Color for plot
opacity

Opacity for plot
strokeColor

The color for stroke
strokeWidth

The width for stroke
strokeType

Line type for stroke, could be linear, cardinal, basis and monotone
animationDisplay

Whether display animation
animationTime, animationDelay, animationType

The time, delay and display type for animation
data

A list of value with details including chr, pos, des, value and html. Details can be found on document
...

Ignored

Value

The module tracks for wig modules

Examples

wigData<-wigExample
Circos(CircosWig('WIG01', data = wigData, maxRadius= 200,minRadius= 150,strokeColor= "darkblue",
color= "lightblue",strokeType= "cardinal")+CircosBackground('BG01',minRadius = 205,maxRadius = 150)
,genome=list("chr8"=1000),outerRadius = 220)

Cnv module example data

Description

The data is in matrix with column names

Usage

cnvExample

Format

A data frame with 7 columns:

chr

chromosome

start

start position

end

end position

value

value

link

hyperlink for cnv

color

color

html

The external html language

Gene plot example data

Description

The data is in matrix with column names

Usage

geneExample

Format

A data frame with 8 columns:

chr

chromosome

strand

strand, - or +

start

start position

end

end position

type

region type, gene or utr or cds

name

name for description

link

hyperlink for this region

html

The external html language

Heatmap plot example data

Description

The data is in matrix with column names

Usage

heatmapExample

Format

A data frame with 7 columns:

chr

chromosome

start

start position

end

end position

name

name for description

value

value

layer

layer number

html

The external html language

Ideogram for hg19

Description

The ideogram for human hg19 reference including the color for each region

Usage

hg19_ideogram

Format

A data frame with 4 columns:

chr

chromosome

start

start position

end

end position

color

color

Histogram plot example data

Description

The data is in matrix with column names

Usage

histogramExample

Format

A data frame with 7 columns:

chr

chromosome

start

start position

end

end position

name

name for description

link

hyperlink

value

value

html

The external html language

Line plot example data

Description

The data is in matrix with column names

Usage

lineExample

Format

A data frame with 5 columns:

chr

chromosome

pos

position

des

description

value

value

html

The external html language

Link plot example data

Description

The data is in matrix with column names

Usage

linkExample

Format

A data frame with 11 columns:

g1chr

first chromosome

g1start

first start position

g1end

first end position

g2chr

second chromosome

g2start

second start position

g2end

second end position

g1name

first name

g2name

second name

fusion

fusion name

link

hyperlink for link line

html

The external html language

Lollipop plot example data

Description

The data is in matrix with column names

Usage

lollipopExample

Format

A data frame with 12 columns:

protein

protein name

chr

chromosome

pos

position

strand

strand, - or +

CancerTypeNumber

Cancer type number

color

color

link

hyperlink

Consequence

consequence

AA_pos

AA_pos

AA_change

AA_change

type

type for mutation,Hetero or Homo

html

The external html language

Scatter plot example data

Description

The data is in matrix with column names

Usage

scatterExample

Format

A data frame with 7 columns:

chr

chromosome

start

start position

end

end position

name

name for scatter

des

description

link

hyperlink

html

The external html language

Snp plot example data

Description

The data is in matrix with column names

Usage

snpExample

Format

A data frame with 10 columns:

chr

chromosome

pos

position

value

value,such as p-value

des

description

color

color

r2value

r2 value

link

hyperlink for snp

index

index for combination

image

image for combination

html

The external html language

Wig plot example data

Description

The data is in matrix with column names

Usage

wigExample

Format

A data frame with 5 columns:

chr

chromosome

pos

position

des

description

value

value

html

The external html language