CircosLollipop {interacCircos} | R Documentation |
Create a lollipop plot
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, ... )
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 |
The module tracks for lollipop modules.
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"))