circos.par {circlize}R Documentation

Parameters for the circular layout

Description

Parameters for the circular layout

Usage

circos.par(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

...

Arguments for the parameters, see "details" section

RESET

reset to default values

READ.ONLY

please ignore

LOCAL

please ignore

ADD

please ignore

Details

Global parameters for the circular 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.

gap.after

identical to gap.degree option, but a more understandable name. Modifying this option will also affect gap.degree.

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. convert_height can be used to set to an absolute unit (e.g cm/inche).

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. Similar as track.margin option, the first and the third value can be set by convert_height to an absolute unit.

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. convert_height can be used to set the height to an absolute unit.

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 and printing 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.

circle.margin

Margin in the horizontal and vertical direction. The value should be a positive numeric vector and the length of it should be either 1, 2, or 4. When it has length of 1, it controls the margin on the four sides of the circle. When it has length of 2, the first value controls the margin on the left and right, and the second value controls the margin on the bottom and top side. When it has length of 4, the four values controls the margins on the left, right, bottom and top sides of the circle. So A value of c(x1, x2, y1, y2) means circos.par(canvas.xlim = c(-(1+x1), 1+x2), canvas.ylim = c(-(1+y1), 1+y2)).

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.

xaxis.clock.wise

The direction in the x-axes for all 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 the circular 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.

See Also

https://jokergoo.github.io/circlize_book/book/circular-layout.html#graphic-parameters

Examples

circos.par

[Package circlize version 0.4.13 Index]