Description Usage Arguments Details Author(s) Examples
Draw arrow which is paralle to the circle
1 2 3 4 5 6 | circos.arrow(x1, x2, y = get.cell.meta.data("ycenter", sector.index, track.index),
width = get.cell.meta.data("yrange", sector.index, track.index)/2,
sector.index = get.current.sector.index(), track.index = get.current.track.index(),
arrow.head.length = convert_x(5, "mm", sector.index, track.index),
arrow.head.width = width*2, arrow.position = c("end", "start"),
tail = c("normal", "point"), border = "black", col = "white", lty = par("lty"), ...)
|
x1 |
start position of the arrow on the x-axis. |
x2 |
end position of the arrow on the x-axis. |
y |
position of the arrow on the y-axis. Note this is the center of the arrow on y-axis. |
width |
width of the arrow body. |
sector.index |
index of the sector. |
track.index |
index of the track. |
arrow.head.length |
length of the arrow head. Note the value should be smaller than the length of the arrow itself (which is |
arrow.head.width |
width of the arrow head. |
arrow.position |
where is the arrow head on the arrow. |
tail |
the shape of the arrow tail (the opposite side of arrow head). |
border |
border color of the arrow. |
col |
filled color of the arrow. |
lty |
line style of the arrow. |
... |
pass to |
Note all position values are measured in the data coordinate (the coordinate in each cell).
If you see points overflow warnings, you can set circos.par(points.overflow.warning = FALSE)
to turn it off.
Zuguang Gu <z.gu@dkfz.de>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | circos.initialize(letters[1:4], xlim = c(0, 1))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
circos.arrow(0, 1, y = 0.5, width = 0.4, arrow.head.length = ux(1, "cm"),
col = "red", tail = ifelse(CELL_META$sector.index %in% c("a", "c"),
"point", "normal"))
}, bg.border = NA, track.height = 0.4)
########## cell cycle ###########
cell_cycle = data.frame(phase = factor(c("G1", "S", "G2", "M"),
levels = c("G1", "S", "G2", "M")),
hour = c(11, 8, 4, 1))
color = c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3")
circos.par(start.degree = 90)
circos.initialize(cell_cycle$phase, xlim = cbind(rep(0, 4), cell_cycle$hour))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
circos.arrow(CELL_META$xlim[1], CELL_META$xlim[2],
arrow.head.width = CELL_META$yrange*0.8, arrow.head.length = ux(1, "cm"),
col = color[CELL_META$sector.numeric.index])
circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index,
facing = "downward")
}, bg.border = NA, track.height = 0.3)
circos.clear()
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.