circos.par.RdParameters for the circular layout
circos.par(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)
| ... | Arguments for the parameters, see "details" section |
|---|---|
| RESET | reset to default values |
| READ.ONLY | please ignore |
| LOCAL | please ignore |
| ADD | please ignore |
Global parameters for the circular layout. Currently supported parameters are:
start.degreeThe 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.degreeGap 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.afteridentical to gap.degree option, but a more understandable name. Modifying this option will also affect gap.degree.
track.marginLike 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.segmentsSince 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.paddingPadding 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.heightThe 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.warningSince 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.marginMargin 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.xlimThe 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.ylimThe coordinate for the canvas. By default it is c(-1, 1)
clock.wiseThe direction for adding sectors. Default is TRUE.
xaxis.clock.wiseThe 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.
circos.par#> Option Value #> -----------------------:------------------ #> start.degree 0 #> gap.degree 1 #> gap.after 1 #> track.margin 0.01, 0.01 #> unit.circle.segments 500 #> cell.padding 0.02, 1, 0.02, 1 #> track.height 0.2 #> points.overflow.warning TRUE #> circle.margin 0, 0, 0, 0 #> canvas.xlim -1, 1 #> canvas.ylim -1, 1 #> major.by.degree 10 #> clock.wise TRUE #> xaxis.clock.wise TRUE #> message TRUE