circlize: Circular Visualization

Description Usage Arguments Details References See Also Examples

Draw links between points or/and intervals

circos.link(sector.index1, point1, sector.index2, point2,
    rou = get_most_inside_radius(),
    rou1 = rou, rou2 = rou, h = NULL, w = 1, h2 = h, w2 = w,
    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)

`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.
`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.
`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`.

Links are implemented as quadratic Bezier curves (https://en.wikipedia.org/wiki/B%C3%A9zier_curve#Rational_B.C3.A9zier_curves ).

Drawing links does not create any track. So you can think it is independent of the tracks.

By default you only need to set sector.index1, point1, sector.index2 and point2. The links would look nice.

Please refer to the vignette for detailed explanation.

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

http://jokergoo.github.io/circlize_book/book/graphics.html#links

factors = letters[1:8]
circos.par(points.overflow.warning = FALSE)
circos.initialize(factors = factors, xlim = c(0, 10))
circos.track(factors = factors, ylim = c(0, 1), bg.col = "grey", 
    bg.border = NA, track.height = 0.05)
circos.link("a", 5, "c", 5, border = 1)
circos.link("b", 5, "d", c(4, 6), border = 1)
circos.link("a", c(2, 3), "f", c(4, 6), border = 1)
circos.link("e", c(2, 3), "g", 5, border = 1)
circos.clear()

circos.par(points.overflow.warning = FALSE)
circos.initialize(factors = factors, xlim = c(0, 10))
circos.track(factors = factors, ylim = c(0, 1), bg.col = "grey", 
    bg.border = NA, track.height = 0.05)
circos.link("a", 5, "b", 5, directional = 1, arr.length = 0.2)
circos.link("c", c(3, 7), "d", c(3, 7), directional = 1, 
    arr.col = "white", arr.length = 0.2)
circos.link("e", c(4, 6), "f", c(4, 6), directional = 1, 
    arr.type = "big.arrow", arr.length = 0.04)
circos.clear()