Description Usage Arguments Details References See Also Examples
Draw links between points or/and intervals
1 2 3 4 5 6 7 | 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,
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 |
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. |
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 |
arr.width |
Width of the arrows, pass to |
arr.type |
Type of the arrows, pass to |
arr.length |
Length of the arrows, measured in 'cm', pass to |
arr.col |
Color of the arrows, pass to |
arr.lwd |
Line width of arrows, pass to |
arr.lty |
Line type of arrows, pass to |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | 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()
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