circos.par(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE)
Arguments
...
Arguments for the parameters, see "details" section
RESET
reset to default values
READ.ONLY
whether only return read-only options
LOCAL
switch local mode
Details
Global parameters for the circos layout. Currently supported parameters are:
start.degree
The starting degree from which the circle begins to draw. Note this degree is measured
in the standard polar coordinate which means it is always reverse-clockwise.
gap.degree
Gap between two neighbour sectors. It can be a single value or a vector. If it is a vector,
the first value corresponds to the gap after the first sector.
track.margin
Like margin in Cascading Style Sheets (CSS), it is the blank area
out of the plotting region, also outside of the borders. Since left and right margin are controlled
by gap.degree, only bottom and top margin need to be set. And all cells in a same track share the same margins, and
that's why this parameter is called track.margin. The value for the track.margin
is the percentage according to the radius of the unit circle.
unit.circle.segments
Since curves are simulated by a series of straight lines,
this parameter controls the amount of segments to represent a curve. The minimal length
of the line segmentation is the length of the unit circle (2pi) divided by unit.circoe.segments.
More segments means better approximation for the curves while larger size if you generate figures as PDF format.
cell.padding
Padding of the cell. Like padding in Cascading Style Sheets
(CSS), it is the blank area around the plotting regions, but within the borders.
The parameter has four values, which controls the bottom, left, top and right paddings
respectively. The first and the third padding
values are the percentages according to the radius of the unit circle and the second and
fourth values are degrees.
track.height
The default height of tracks. It is the percentage according to the radius
of the unit circle. The height includes the top and bottom cell paddings but not the margins.
points.overflow.warning
Since each cell is in fact not a real plotting region but only
an ordinary rectangle, it does not eliminate points that are plotted out of
the region. So if some points are out of the plotting region, circlize would continue drawing the points but print warnings. In some
cases, draw something out of the plotting region is useful, such as draw
some legend or text. Set this value to FALSE to turn off the warnings.
canvas.xlim
The coordinate for the canvas. Because circlize draws everything (or almost everything) inside the unit circle,
the default canvas.xlim and canvas.ylim for the canvas would be all c(-1, 1). However, you can set it to a more broad
interval if you want to draw other things out of the circle. By choosing proper
canvas.xlim and canvas.ylim, you can draw part of the circle. E.g. setting
canvas.xlim to c(0, 1) and canvas.ylim to c(0, 1) would only draw
circle in the region of (0, pi/2).
canvas.ylim
The coordinate for the canvas. By default it is c(-1, 1)
clock.wise
The direction for adding sectors. Default is TRUE.
Similar as par, you can get the parameter values by specifying the
names of parameters and you can set the parameter values by specifying a
named list which contains the new values.
gap.degree, start.degree, canvas.xlim, canvas.ylim and clock.wise
only be set before the initialization of circos layout
(i.e. before calling circos.initialize) because these values will not be changed after
adding sectors on the circle. The left and right padding for cell.padding will also be
ignored after the initialization because all cells in a sector would share the same
left and right paddings.
References
Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.
providing 
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