interacCircos (version 1.0.0)

CircosGene: Create a GENE module to a moduleList

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

# NOT RUN {
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)

# }