CircosSnp {interacCircos} | R Documentation |
Create SNPs are defined by genomic coordinates and associated with a numerical value
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, ... )
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 |
The module tracks for snp modules
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))