interacCircos (version 1.0.0)

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

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

# NOT RUN {
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))

# }