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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
ccCell. Any
ccCellGeom and ccCells are added together as
if they were added to each ccCell contained in the
ccCells.| 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:
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)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)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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