circos.axis {circlize}

Draw x-axis

Description

Draw x-axis

Usage

circos.axis(
    h = "top",
    major.at = NULL,
    labels = TRUE,
    major.tick = TRUE,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    labels.font = par("font"),
    labels.cex = par("cex"),
    labels.facing = "inside",
    labels.direction = NULL,
    labels.niceFacing = TRUE,
    direction = c("outside", "inside"),
    minor.ticks = 4,
    major.tick.length = mm_y(1),
    major.tick.percentage = 0.5,
    lwd = par("lwd"),
    col = par("col"),
    labels.col = par("col"),
    labels.pos.adjust = TRUE)

Arguments

h

Position of the x-axis, can be "top", "bottom" or a numeric value

major.at

If it is numeric vector, it identifies the positions of the major ticks. It can exceed xlim value and the exceeding part would be trimmed automatically. If it is NULL, about every 10 degrees there is a major tick.

labels

labels of the major ticks. Also, the exceeding part would be trimmed automatically. The value can also be logical (either an atomic value or a vector) which represents which labels to show.

major.tick

Whether to draw major tick. If it is set to FALSE, there will be no minor ticks neither.

sector.index

Index for the sector.

track.index

Index for the track.

labels.font

Font style for the axis labels.

labels.cex

Font size for the axis labels.

labels.direction

Deprecated, use facing instead.

labels.facing

Facing of labels on axis, passing to circos.text

labels.niceFacing

Should facing of axis labels be human-easy.

direction

Whether the axis ticks point to the outside or inside of the circle.

minor.ticks

Number of minor ticks between two close major ticks.

major.tick.length

Length of the major ticks, measured in "current" data coordinate. convert_y can be used to convert an absolute unit to the data coordinate.

major.tick.percentage

Not used any more, please directly use major.tick.length.

lwd

Line width for ticks.

col

Color for the axes.

labels.col

Color for the labels.

labels.pos.adjust

Whether to adjust the positions of the first label and the last label so that the first label align to its left and the last label align to its right if they exceed the range on axes. The value can be a vector of length two which correspond to the first label and the last label.

Details

It only draws axes on x-direction.

See Also

circos.yaxis draws axes on y-direction.

https://jokergoo.github.io/circlize_book/book/graphics.html#axes

Examples

sectors = letters[1:8]
circos.par(points.overflow.warning = FALSE)
circos.initialize(sectors, xlim = c(0, 10))
circos.trackPlotRegion(sectors, ylim = c(0, 10), track.height = 0.1,
    bg.border = NA, panel.fun = function(x, y) {
        circos.text(5, 10, get.cell.meta.data("sector.index"))
})

circos.trackPlotRegion(sectors, ylim = c(0, 10))
circos.axis(sector.index = "a")
circos.axis(sector.index = "b", direction = "inside", labels.facing = "outside")
circos.axis(sector.index = "c", h = "bottom")
circos.axis(sector.index = "d", h = "bottom", direction = "inside",
    labels.facing = "reverse.clockwise")
circos.axis(sector.index = "e", h = 5, major.at = c(1, 3, 5, 7, 9))
circos.axis(sector.index = "f", h = 5, major.at = c(1, 3, 5, 7, 9),
    labels = c("a", "c", "e", "g", "f"), minor.ticks = 0)
circos.axis(sector.index = "g", h = 5, major.at = c(1, 3, 5, 7, 9),
    labels = c("a1", "c1", "e1", "g1", "f1"), major.tick = FALSE,
    labels.facing = "reverse.clockwise")
circos.axis(sector.index = "h", h = 2, major.at = c(1, 3, 5, 7, 9),
    labels = c("a1", "c1", "e1", "g1", "f1"), minor.ticks = 2, 
    major.tick.length = mm_y(5), labels.facing = "clockwise")
circos.clear()

if(FALSE) {

############### real-time clock #################
factors = letters[1]

circos.par("gap.degree" = 0, "cell.padding" = c(0, 0, 0, 0), "start.degree" = 90)
circos.initialize(sectors, xlim = c(0, 12))
circos.trackPlotRegion(sectors, ylim = c(0, 1), bg.border = NA)
circos.axis(sector.index = "a", major.at = 0:12, labels = "",
    direction = "inside", major.tick.length = mm_y(3))
circos.text(1:12, rep(0.5, 12), 1:12, facing = "downward")

while(1) {
    current.time = as.POSIXlt(Sys.time())
    sec = ceiling(current.time$sec)
    min = current.time$min
    hour = current.time$hour

    # erase the clock hands
    draw.sector(rou1 = 0.8, border = "white", col = "white")

    sec.degree = 90 - sec/60 * 360
    arrows(0, 0, cos(sec.degree/180*pi)*0.8, sin(sec.degree/180*pi)*0.8)

    min.degree = 90 - min/60 * 360
    arrows(0, 0, cos(min.degree/180*pi)*0.7, sin(min.degree/180*pi)*0.7, lwd = 2)

    hour.degree = 90 - hour/12 * 360 - min/60 * 360/12
    arrows(0, 0, cos(hour.degree/180*pi)*0.4, sin(hour.degree/180*pi)*0.4, lwd = 2)

    Sys.sleep(1)
}
circos.clear()
}