CircosGene: Create a GENE module to a moduleList

In interacCircos: The Visualization of Interactive Circos Plot

Description

A number of genes with different functional region displayed in the visualization

Usage

CircosGene(
  modulename,
  compareGroup = 1,
  outerRadius = 180,
  innerRadius = 150,
  pathColor = "black",
  pathWidth = 1,
  arrow = TRUE,
  arrowGap = 2,
  arrowColor = "blue",
  arrowSize = 5,
  cdsColor = "#1e77b3",
  cdsStrokeColor = "black",
  cdsStrokeWidth = 1,
  utrWidth = -5,
  utrColor = "blue",
  utrStrokeColor = "blue",
  utrStrokeWidth = 1,
  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
outerRadius, innerRadius	Where the module should begin and end.
pathColor	The color for path between gene elements
pathWidth	The width for path between gene elements
arrow	Whether display arrows on path
arrowGap, arrowColor, arrowSize	The gap, color and size for arrow
cdsColor, cdsStrokeColor, cdsStrokeWidth	The color, stroke color and stroke width for coding
utrWidth, utrColor, utrStrokeColor, utrStrokeWidth	The max size for bubble
animationDisplay	Whether display animation
animationTime, animationDelay, animationType	The time, delay and display type for animation
data	A list of gene with details including chr, strand, start, end, type, name, link and html. Details can be found on document.
...	Ignored

Value

The module tracks for gene modules.

Examples

geneData<-geneExample
Circos(CircosGene('Gene01', outerRadius = 195, innerRadius = 180, data=geneData,arrowGap = 10,
 arrowColor = "black",arrowSize = "12px",cdsColor = "#1e77b3",cdsStrokeColor = "#1e77b3",
 cdsStrokeWidth= 5, utrWidth= -2,utrColor= "#fe7f0e",utrStrokeColor= "#fe7f0e",
 animationDisplay = TRUE),genome =list("EGFR"=1000), outerRadius = 220)

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