circos.axis: Draw x-axis

Description

Draw x-axis

Usage

circos.axis(h = "top", major.at = NULL, labels = TRUE, major.tick = TRUE,
    sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("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.percentage = 0.1, labels.away.percentage = major.tick.percentage/2,
    major.tick.length = convert_y(1, "mm", sector.index, track.index),
    lwd = par("lwd"), col = par("col"), labels.col = par("col"))

Arguments

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 would be no minor ticks.

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.percentage

not used. Length of the major ticks. It is the percentage to the height of the cell.

labels.away.percentage

not used. The distance for the axis labels to the major ticks. It is the percentage to the height of the cell.

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.

lwd

line width for ticks

col

color for the axes

labels.col

color for the labels

Details

It can only draw axes on x-direction.

References

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

Examples

Run this code

# NOT RUN {
factors = letters[1:8]
circos.par(points.overflow.warning = FALSE)
circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, 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(factors = factors, 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"), major.tick.percentage = 0.3,
    labels.away.percentage = 0.2, minor.ticks = 2, labels.facing = "clockwise")
circos.clear()

# }
# NOT RUN {
############### real-time clock #################
factors = letters[1]

circos.par("gap.degree" = 0, "cell.padding" = c(0, 0, 0, 0), "start.degree" = 90)
circos.initialize(factors = factors, xlim = c(0, 12))
circos.trackPlotRegion(factors = factors, ylim = c(0, 1), bg.border = NA)
circos.axis(sector.index = "a", major.at = 0:12, labels = "",
    direction = "inside", major.tick.percentage = 0.3)
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()

# }
# NOT RUN {
# }