circos.arrow: Draw arrow which is paralle to the circle

In jokergoo/circlize: Circular Visualization

Draw arrow which is paralle to the circle

Description

Draw arrow which is paralle to the circle

Usage

circos.arrow(
    x1,
    x2,
    y = get.cell.meta.data("ycenter"),
    width = get.cell.meta.data("yrange")/2,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    arrow.head.length = mm_x(5),
    arrow.head.width = width*2,
    arrow.position = c("end", "start"),
    tail = c("normal", "point"),
    border = "black",
    col = "#FFCCCC",
    lty = par("lty"),
    ...)

Arguments

x1	Start position of the arrow on the x-axis.
x2	End position of the arrow on the x-axis. Note x2 should be larger than x1. The direction of arrows can be controlled by arrow.position argument.
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 x2 - x1).
arrow.head.width	Width of the arrow head.
arrow.position	Where is the arrow head on the arrow. If you want to the arrow in the reversed direction, set this value to "start".
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 polygon.

Details

Note all position values are measured in the data coordinate (the coordinate in each cell). For the values of width, arrow.head.Length, arrow.head.width, they can be set with mm_y/cm_y/inches_y in absolute units.

If you see points overflow warnings, you can set circos.par(points.overflow.warning = FALSE) to turn it off.

Author(s)

Zuguang Gu <[e-mail]>

See Also

https://jokergoo.github.io/circlize_book/book/graphics.html#circular-arrows

Examples

op = par(no.readonly = TRUE)
par(mfrow = c(1, 2))
circos.initialize(letters[1:4], xlim = c(0, 1))
col = rand_color(4)
tail = c("point", "normal", "point", "normal")
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4, 
        arrow.head.width = 0.6, arrow.head.length = cm_x(1), 
        col = col[CELL_META$sector.numeric.index], 
        tail = tail[CELL_META$sector.numeric.index])
}, bg.border = NA, track.height = 0.4)
circos.clear()

circos.initialize(letters[1:4], xlim = c(0, 1))
tail = c("point", "normal", "point", "normal")
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
    circos.arrow(x1 = 0, x2 = 1, y = 0.5, width = 0.4, 
        arrow.head.width = 0.6, arrow.head.length = cm_x(1), 
        col = col[CELL_META$sector.numeric.index], 
        tail = tail[CELL_META$sector.numeric.index],
        arrow.position = "start")
}, bg.border = NA, track.height = 0.4)
par(op)

########## 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$yrange*0.8, arrow.head.length = cm_x(1),
      col = color[CELL_META$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()

jokergoo/circlize documentation built on Nov. 17, 2023, 11:32 a.m.