circos.connect {circlize}R Documentation

Draw connecting lines/ribons between two sets of points

Description

Draw connecting lines/ribons between two sets of points

Usage

circos.connect(x0, y0, x1, y1,
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    type = c("normal", "segments", "bezier"),
    segments.ratio = c(1, 1, 1),
    col = par("col"),
    border = "black",
    lwd = par("lwd"),
    lty = par("lty"),
    ...)

Arguments

x0

x coordinates for point set 1. The value can also be a two-column matrix.

y0

y coordinates for point set 1.

x1

x coordinates for point set 2. The value can also be a two-column matrix.

y1

y coordinates for point set 2.

sector.index

Index for the sector.

track.index

Index for the track.

type

Which type of connections. Values can be "normal", "segments" and "bezier".

segments.ratio

When type is set to segments, each connecting line is segmented into three parts. This argument controls the length of the three parts of sub-segments.

col

Color of the segments.

border

Border color of the links.

lwd

Line width of the segments.

lty

Line type of the segments.

...

Other arguments.

Examples


circos.initialize(c("a"), xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.7, bg.border = NA, 
    panel.fun = function(x, y) {
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[1], 2), col = "#CCCCCC")
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[2], 2), col = "#CCCCCC")
    x0 = runif(100)
    x1 = runif(100)

circos.connect(x0, 0, x1, 1, 
        type = "normal", border = NA,
        col = rand_color(100, luminosity = "bright", transparency = 0.75))
})

circos.initialize(c("a"), xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.7, bg.border = NA, 
    panel.fun = function(x, y) {
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[1], 2), col = "#CCCCCC")
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[2], 2), col = "#CCCCCC")
    x0 = runif(100)
    x1 = runif(100)

circos.connect(x0, 0, x1, 1, 
        type = "bezier", border = NA,
        col = rand_color(100, luminosity = "bright", transparency = 0.75))
})

circos.initialize(c("a"), xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.7, bg.border = NA, 
    panel.fun = function(x, y) {
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[1], 2), col = "#CCCCCC")
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[2], 2), col = "#CCCCCC")
    x0 = sort(runif(200))
    x0 = matrix(x0, ncol = 2, byrow = TRUE)
    x1 = sort(runif(200))
    x1 = matrix(x1, ncol = 2, byrow = TRUE)

circos.connect(x0, 0, x1, 1, 
        type = "normal", border = NA,
        col = rand_color(100, luminosity = "bright", transparency = 0.5))
})

circos.initialize(c("a"), xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.7, bg.border = NA, 
    panel.fun = function(x, y) {
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[1], 2), col = "#CCCCCC")
    circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[2], 2), col = "#CCCCCC")
    x0 = sort(runif(500))
    x0 = matrix(x0, ncol = 2, byrow = TRUE)
    x0 = x0[sample(nrow(x0), nrow(x0)), ]
    x1 = sort(runif(500))
    x1 = matrix(x1, ncol = 2, byrow = TRUE)
    x1 = x1[sample(nrow(x1), nrow(x1)), ]

l = abs(x0[, 1] - x1[, 1]) < 0.5

circos.connect(x0[l ,], 0, x1[l, ], 1, 
        type = "bezier", border = NA,
        col = rand_color(sum(l), luminosity = "bright", transparency = 0.5))
})


[Package circlize version 0.4.13 Index]