circlize (version 0.4.1)

circos.lines: Add lines to the plotting region

Description

Add lines to the plotting region

Usage

circos.lines(x, y, sector.index = get.cell.meta.data("sector.index"),
    track.index = get.cell.meta.data("track.index"),
    col = ifelse(area, "grey", par("col")), lwd = par("lwd"), lty = par("lty"),
    type = "l", straight = FALSE, area = FALSE, area.baseline = NULL,
    border = "black", baseline = "bottom", pt.col = par("col"), cex = par("cex"),
    pch = par("pch"))

Arguments

x

Data points on x-axis, measured in "current" data coordinate

y

Data points on y-axis, measured in "current" data coordinate

sector.index

Index for the sector

track.index

Index for the track

col

Line color

lwd

line width

lty

line style

type

line type, similar as type argument in lines, but only in c("l", "o", "h", "s")

straight

whether draw straight lines between points.

area

whether to fill the area below the lines. If it is set to TRUE, col controls the filled color in the area and border controls color of the line.

area.baseline

deprecated, use baseline instead.

baseline

the base line to draw areas. By default it is the minimal of y-range (bottom). It can be a string or a number. If a string, it should be one of bottom and top. This argument also works if type is set to h.

border

color for border of the area

pt.col

if type is "o", point color

cex

if type is "o", point size

pch

if type is "o", point type

Details

Normally, straight lines in the Cartesian coordinate have to be transformed into curves in the circular layout. But if you do not want to do such transformation you can use this function just drawing straight lines between points by setting straight to TRUE.

Drawing areas below lines can help to identify the direction of y-axis in cells (since it is a circle). This can be done by specifying area to TURE.

References

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

Examples

# NOT RUN {
factors = letters[1:9]
circos.par(points.overflow.warning = FALSE)
circos.initialize(factors = factors, xlim = c(0, 10))
circos.trackPlotRegion(factors = factors, ylim = c(0, 10), track.height = 0.5)

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "a")
circos.text(5, 9, "type = 'l'", sector.index = "a", facing = "outside")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "b", type = "o")
circos.text(5, 9, "type = 'o'", sector.index = "b", facing = "outside")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "c", type = "h")
circos.text(5, 9, "type = 'h'", sector.index = "c", facing = "outside")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "d", type = "h", baseline = 5)
circos.text(5, 9, "type = 'h', baseline = 5", sector.index = "d", facing = "outside")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "e", type = "s")
circos.text(5, 9, "type = 's'", sector.index = "e", facing = "outside")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "f", area = TRUE)
circos.text(5, 9, "type = 'l', area = TRUE", sector.index = "f")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "g", type = "o", area = TRUE)
circos.text(5, 9, "type = 'o', area = TRUE", sector.index = "g")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "h", type = "s", area = TRUE)
circos.text(5, 9, "type = 's', area = TRUE", sector.index = "h")

circos.lines(sort(runif(10)*10), runif(10)*8, sector.index = "i", area = TRUE, baseline = "top")
circos.text(5, 9, "type = 'l', area = TRUE\nbaseline = 'top'", sector.index = "i")

circos.clear()

# }