CircosSnp: Create a module with SNPs to be added to a moduleList

In interacCircos: The Visualization of Interactive Circos Plot

Description

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))

interacCircos documentation built on Jan. 21, 2021, 5:10 p.m.