\name{circos.par}
\alias{circos.par}
\title{
Parameters for the circular layout
}
\description{
Parameters for the circular layout
}
\usage{
circos.par(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)
}
\arguments{

  \item{...}{Arguments for the parameters, see "details" section
}
  \item{RESET}{reset to default values
}
  \item{READ.ONLY}{please ignore
}
  \item{LOCAL}{please ignore
}
  \item{ADD}{please ignore
}

}
\details{
Global parameters for the circular layout. Currently supported parameters are:

\describe{
  \item{\code{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.
}
  \item{\code{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.
}
  \item{\code{gap.after}}{identical to \code{gap.degree} option, but a more understandable name. Modifying this option will also affect \code{gap.degree}.
}
  \item{\code{track.margin}}{Like \code{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 \code{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 \code{track.margin}. The value for the \code{track.margin}
 is the percentage according to the radius of the unit circle. \code{\link{convert_height}} can be used to set to an absolute unit (e.g cm/inche).
}
  \item{\code{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 (\code{2pi}) divided by \code{unit.circoe.segments}.
 More segments means better approximation for the curves while larger size if you generate figures as PDF format.
}
  \item{\code{cell.padding}}{Padding of the cell. Like \code{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 \code{track.margin} option, the first and the third value
 can be set by \code{\link{convert_height}} to an absolute unit.
}
  \item{\code{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.
 \code{\link{convert_height}} can be used to set the height to an absolute unit.
}
  \item{\code{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, \code{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 \code{FALSE} to turn off the warnings.
}
  \item{\code{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 \code{c(x1, x2, y1, y2)} means \code{circos.par(canvas.xlim = c(-(1+x1), 1+x2), canvas.ylim = c(-(1+y1), 1+y2))}.
}
  \item{\code{canvas.xlim}}{The coordinate for the canvas. Because \code{circlize} draws everything (or almost everything) inside the unit circle,
 the default \code{canvas.xlim} and \code{canvas.ylim} for the canvas would be all \code{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
 \code{canvas.xlim} and \code{canvas.ylim}, you can draw part of the circle. E.g. setting
 \code{canvas.xlim} to \code{c(0, 1)} and \code{canvas.ylim} to \code{c(0, 1)} would only draw
 circle in the region of (0, pi/2).
}
  \item{\code{canvas.ylim}}{The coordinate for the canvas. By default it is \code{c(-1, 1)}
}
  \item{\code{clock.wise}}{The direction for adding sectors. Default is \code{TRUE}.
}
  \item{\code{xaxis.clock.wise}}{The direction in the x-axes for all sectors. Default is \code{TRUE}.
}
}

Similar as \code{\link[graphics]{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.

\code{gap.degree}, \code{start.degree}, \code{canvas.xlim}, \code{canvas.ylim} and \code{clock.wise}
only be set before the initialization of the circular layout
(i.e. before calling \code{\link{circos.initialize}}) because these values will not be changed after
adding sectors on the circle. The left and right padding for \code{cell.padding} will also be
ignored after the initialization because all cells in a sector would share the same
left and right paddings.
}
\seealso{
\url{https://jokergoo.github.io/circlize_book/book/circular-layout.html#graphic-parameters}
}
\examples{
circos.par
}
