circlize: Circular Visualization

circos.link

R Documentation

Draw links between points or/and intervals

Description

Draw links between points or/and intervals

Usage

circos.link(
    sector.index1,
    point1,
    sector.index2,
    point2,
    rou = get_most_inside_radius(),
    rou1 = rou,
    rou2 = rou,
    h = NULL,
    h.ratio = 0.5,
    w = 1,
    h2 = h,
    w2 = w,
    inverse = FALSE,
    col = "black",
    lwd = par("lwd"),
    lty = par("lty"),
    border = col,
    directional = 0,
    arr.length = ifelse(arr.type == "big.arrow", 0.02, 0.4),
    arr.width = arr.length/2,
    arr.type = "triangle",
    arr.lty = lty,
    arr.lwd = lwd,
    arr.col = col,
    reduce_to_mid_line = FALSE)

Arguments

`sector.index1`	Index for the first sector where one link end locates
`point1`	A single value or a numeric vector of length 2. If it is a 2-elements vector, then the link would be a belt/ribbon.
`sector.index2`	Index for the other sector where the other link end locates
`point2`	A single value or a numeric vector of length 2. If it is a 2-elements vector, then the link would be a belt/ribbon.
`rou`	The position of the the link ends (if `rou1` and `rou2` are not set). It is the percentage of the radius of the unit circle. By default its value is the position of bottom margin of the most inner track.
`rou1`	The position of end 1 of the link.
`rou2`	The position of end 2 of the link.
`h`	Height of the link, measured as percent to the radius to the unit circle. By default it is automatically infered.
`h.ratio`	systematically change the link height. The value is between 0 and 1.
`w`	Since the link is a Bezier curve, it controls the shape of Bezier curve.
`h2`	Height of the bottom edge of the link if it is a ribbon.
`w2`	Shape of the bottom edge of the link if it is a ribbon.
`inverse`	Whether the link is inversed.
`col`	Color of the link. If the link is a ribbon, then it is the filled color for the ribbon.
`lwd`	Line (or border) width
`lty`	Line (or border) style
`border`	If the link is a ribbon, then it is the color for the ribbon border.
`directional`	0 for no direction, 1 for direction from `point1` to `point2`, -1 for direction from `point2` to `point1`. 2 for two directional. The direction is important when arrow heads are added.
`arr.width`	Width of the arrows, pass to `Arrowhead`.
`arr.type`	Type of the arrows, pass to `Arrowhead`. Default value is `triangle`. There is an additional option `big.arrow`.
`arr.length`	Length of the arrows, measured in 'cm', pass to `Arrowhead`. If `arr.type` is set to `big.arrow`, the value is percent to the radius of the unit circle.
`arr.col`	Color of the arrows, pass to `Arrowhead`.
`arr.lwd`	Line width of arrows, pass to `Arrowhead`.
`arr.lty`	Line type of arrows, pass to `Arrowhead`.
`reduce_to_mid_line`	Only use the middle points of `point1` and `point2` to draw the link.