CircosLollipop: Create a LOLLIPOP module to a moduleList

In interacCircos: The Visualization of Interactive Circos Plot

Description

Display a lollipop plot in the visualization

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"))

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