interacCircos (version 1.0.0)

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

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

# NOT RUN {
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)

# }