Using the circlizePlus Package"

In circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization

Addition rules

ccPlot(contain n ccPars)+ccPar=ccPlot(contain n+1 ccPars),n>=0

ccPlot(contain n ccTracks)+ccTrack=ccPlot(contain n+1 ccTracks),n>=0

ccPlot(contain n ccLinks)+ccLink=ccPlot(contain n+1 ccLinks),n>=0

ccTrak(contain n ccTrakGeoms)+ccTrackGeom=ccTrack(contain n+1 ccTrackGeoms),n>=0

ccTrack(contain n ccCells)+ccCell=ccTrack(contain n+1 ccCells),n>=0

ccCell(contain n ccCellGeoms)+ccCellGeom=ccCell(contain n+1 ccCellGeoms),n>=0

S4 class ccCell and ccCells

• ccCell: Generate a cell container that belongs to a particular sector.
• ccCells: A list of multiple ccCell. Any ccCellGeom and ccCells are added together as if they were added to each ccCell contained in the ccCells.

API outline

Initializer

• Class: ccPlot-class
• Function: ccPlot()

Parameter

• Class: ccPar-class
• Function: ccPar()

Cell container

• Class: ccCell-class, ccCells-class
• Function: ccCell(), ccCells()

Cell geometry

• Class: ccCellGeom-class, ccGenomicCellGeom-class
• Function: ccText(), ccPoints(), ccLines(), ccSegments(), ccRect(), ccPolygon(), ccXaxis(), ccYaxis(), ccBarplot(), ccBoxplot(), ccViolin(), ccArrow(), ccRaster(), ccDendrogram(), ccGenomicPoints(), ccGenomicLines(), ccGenomicRect(), ccGenomicText(), ccGenomicAxis()

Track container

• Class: ccTrack-class, ccGenomicTrack-class
• Function: ccTrack(), ccTrackHist(), ccGenomicTrack(), ccGenomicIdeogram(), ccGenomicHeatmap(), ccGenomicLabels(), ccGenomicRainfall(), ccGenomicDensity()

Track geometry

• Class: ccTrackGeom-class
• Function: ccTrackLines(), ccTrackPoints(), ccTrackText()

Link

• Class: ccLink-class, ccHeatmapLink-class, ccGenomicLink-class
• Function: ccLink(), ccHeatmapLink(), ccGenomicLink()

Heatmap

• Class: ccHeatmap-class
• Function: ccHeatmap()

Data mapping from track to cell geometry

| | | | | | | | | | | | |-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| | ccTrack Constructor | ccGenomicTrack() | ccGenomicTrack() | ccGenomicTrack() | ccGenomicTrack() | ccTrack() | ccTrack() | ccTrack() | ccTrack() | ccTrack() | ccTrack() | | Parameters in ccTrack Constructor | data | data | data | data | x, y | x, y | x, y | x, y | x, y | x, y | | ccCellGeom Constructor | ccGenomicPoints() | ccGenomicLines() | ccGenomicRect() | ccGenomicText() | ccLines() | ccPoints() | ccPolygon() | ccText() | ccRect() | ccSegments() | | Parameters in ccCellGeom Constructor | region, value | region, value | region, value | region, value | x, y | x, y | x, y | x, y | xleft, ybottom, xright, ytop | x0, y0, x1, y1 |

A combination of each column in the table above:

Get track from ccGenomicTrack()

region and value in ccGenomicCellGeom constructor can be NULL or function like function(region,value){...}. The above data can be obtained from the data parameter of ccGenomicTrack.

In the following example code, the region and value in the ccGenomicLines constructor are NULL. Their real data comes from the data value of the corresponding sector in ccGenomicTrack. The region and value in the ccGenomicPoints constructor are function. Their real data is calculated based on the definition of the function.

data = generateRandomBed(nr =30, nc = 2)
all_chr = c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY")
cc = ccPlot(initMode = "initializeWithIdeogram", plotType=NULL)
t1 = ccGenomicTrack(data=data, numeric.column = 4,
                    panel.fun=function(region,value,...){
                      circos.genomicPoints(region,value,...)
                    })
cells1 = ccCells(sector.indexes = all_chr) + ccGenomicLines(numeric.column=2) + ccGenomicPoints(region=\(region,value){region}, value=\(region,value){value}, numeric.column=2)
t1 = t1 + cells1
show(cc+t1)

Get track from ccTrack()

x, x0, x1, xleft, xright, y, y0, y1, ytop, ybottom in ccCellGeom constructor can be NULL or function like function(x,y){...}. The above data can be obtained from the x and y parameter of ccTrack.

In the following example code, the x and y in the first ccPoints constructor are NULL. Their real data comes from the x and y of the corresponding sector in ccTrack. The y in the second ccPoints constructor are function. Their real data is calculated based on the definition of the function.

sectors = c('a','a','a','a','b','b','b','b','c','c','c','c','d','d','d','d')
x1 = c(1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4)
y1 = c(1,2,3,4,4,3,2,1,1,1,1,1,1,2,1,2)
cc = ccPlot(initMode = "initialize", sectors = sectors, x = x1)
cells = ccCells(sector.indexes = letters[1:4])
cc_point = ccPoints()
cells = cells + cc_point + ccLines()
track1 = ccTrack(sectors = sectors, x=x1, y = y1,panel.fun = function(x,y){
  circos.points(y,x)
})
cell_single = ccCell(sector.index = letters[3]) + ccPoints(y=\(x,y){x-y})
track1 = track1 + cells + cell_single
show(cc  + track1)

circlizePlus documentation built on June 8, 2025, 10:42 a.m.