CircosChord: Create a CHORD module of NG-Circos to a moduleList

In interacCircos: The Visualization of Interactive Circos Plot

Description

Display a chord module using a data matrix.

Usage

CircosChord(
  modulename,
  innerRadius = 237,
  outerRadius = 238,
  fillOpacity = 0.67,
  fillStrokeWidth = 1,
  padding = 0.06,
  autoFillColor = TRUE,
  fillColor = c("#B8B8B8"),
  fillStrokeColor = c("black"),
  outerARC = TRUE,
  outerARCAutoColor = TRUE,
  outerARCColor = c("red"),
  outerARCStrokeColor = c("black"),
  outerARCText = TRUE,
  data,
  ...
)

Arguments

modulename	The name of the new module.
innerRadius	The inner radius for chord circle
outerRadius	The outer radius for chord circle
fillOpacity	The opacity for filling color.
fillStrokeWidth	The stroke width for chord.
padding	The pad of chord
autoFillColor	Whether auto assign color for chord
fillColor	If not, manually assign color for chord
fillStrokeColor	The color for stroke
outerARC	Whether display outer arc
outerARCAutoColor	If true, whether auto assign color for arc
outerARCColor	The manullay assigned color for arc
outerARCStrokeColor	The stroke color for arc
outerARCText	Whether display text for arc or not
data	A matrix-list of chord value with relationship details.
...	Ignored

Value

The module tracks for chord modules of NG-Circos.

Examples

chordData<-chordExample
Circos(CircosChord('CHORD', data = chordData,innerRadius= 210,outerRadius= 211,fillOpacity=0.67,
strokeColor="black",strokeWidth= "1px",outerARCText=FALSE),genome=list("C.CK" = 189.51,"C.NPK"=188,
"GC.CK"=186.11, "GC.NPK"=191.51,"Alphaproteobacteria"=70.16,"Betaproteobacteria"=23.51,
"Gammaproteobacteria"=25.51, "Deltaproteobacteria"=23.28,"Acidobacteria"=53.62,
"Actinobacteria"=72.33, "Bacteroidetes"=22.41, "Chloroflexi"=15.08,"Firmicutes"=10.72,
"Gemmatimonadetes"=26.37, "Planctomycetes"=19.26,"Thaumarchaeota"=6.15, "Verrucomicrobia"=8.3,
"Ascomycota"=159.41, "Basidiomycota"=79.73,"Zygomycota"=139.29 ),outerRadius = 217, 
genomeLabelDisplay = FALSE)

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