interacCircos (version 1.0.0)

CircosLollipop: Create a LOLLIPOP module to a moduleList

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

# NOT RUN {
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"))

# }