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add circos.connect() function
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@jokergoo
jokergoo committed Nov 24, 2020
1 parent 70fe713 commit 29f0d69
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6 changes: 3 additions & 3 deletions DESCRIPTION
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@@ -1,15 +1,15 @@
Package: circlize
Type: Package
Title: Circular Visualization
Version: 0.4.12.1001
Date: 2020-11-23
Version: 0.4.12.1002
Date: 2020-11-24
Author: Zuguang Gu
Maintainer: Zuguang Gu <[email protected]>
Depends: R (>= 3.0.0), graphics
Imports: GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats,
colorspace, methods, grid
Suggests: knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase,
png, markdown
png, markdown, bezier
VignetteBuilder: knitr
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -19,6 +19,7 @@ export("circos.axis")
export("circos.barplot")
export("circos.boxplot")
export("circos.clear")
export("circos.connect")
export("circos.dendrogram")
export("circos.genomicAxis")
export("circos.genomicDensity")
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1 change: 1 addition & 0 deletions NEWS
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Expand Up @@ -11,6 +11,7 @@ Changes in version 0.4.12
* `circos.points()`, `circos.lines()`, `circos.text()` allow argument `x` to be
a two-column matrix.
* add `arrange_links_evenly()` function.
* add `circos.connect()` function.

Changes in version 0.4.11
-----------------------------------------------------------------------
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273 changes: 271 additions & 2 deletions R/low_level.R
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Expand Up @@ -750,9 +750,8 @@ circos.segments = function(
return(invisible(NULL))
}


if(!has.cell(sector.index, track.index)) {
stop_wrap("'circos.polygon' can only be used after the plotting region been created.")
stop_wrap("'circos.segments' can only be used after the plotting region been created.")
}

np = length(x0)
Expand Down Expand Up @@ -2323,3 +2322,273 @@ circos.violin = function(value, pos, violin_width = 0.8,
max_d = max(density$y), value = value)
}
}




get_bezier_points = function(x1, y1, x2, y2, xlim, ylim) {

x1 = (x1 - xlim[1])/(xlim[2] - xlim[1])
x2 = (x2 - xlim[1])/(xlim[2] - xlim[1])
y1 = (y1 - ylim[1])/(ylim[2] - ylim[1])
y2 = (y2 - ylim[1])/(ylim[2] - ylim[1])

r = 0.6 - abs(x2 - x1)/2
p = cbind(c(0, 0, 1, 1), c(0, r, r, 1))
pt = bezier::bezier(t = seq(0, 1, length = 50), p = p)

wx = x2 - x1
x = pt[, 1] * wx + x1

wy = y2 - y1
y = pt[, 2]*wy + y1

x = x*(xlim[2] - xlim[1]) + xlim[1]
y = y*(ylim[2] - ylim[1]) + ylim[1]

data.frame(x = x, y = y)
}

# == title
# Draw connecting lines/ribons between two sets of points
#
# == param
# -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.
#
# == example
# 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))
# })
circos.connect = function(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"),
...) {

type = match.arg(type)[1]

if(type == "bezier") {
if(!requireNamespace("bezier")) {
stop_wrap("You need to install 'bezier' package from CRAN.")
}
}

if(is.null(nrow(x0))) {
n1 = length(x0)
} else {
x0 = x0[, 1:2]
n1 = nrow(x0)
}
n2 = length(y0)
if(is.null(nrow(x1))) {
n3 = length(x1)
} else {
x1 = x1[, 1:2]
n3 = nrow(x1)
}
n4 = length(y1)
n = max(c(n1, n2, n3, n4))
if(n1 == 1) {
if(is.null(nrow(x0))) {
x0 = rep(x0, n)
} else {
x0 = matrix(rep(x0, each = n), ncol = 2)
}
n1 = n
}
if(n2 == 1) { y0 = rep(y0, n); n2 = n }
if(n3 == 1) {
if(is.null(nrow(x1))) {
x1 = rep(x1, n)
} else {
x1 = matrix(rep(x1, each = n), ncol = 2)
}
n3 = n
}
if(n4 == 1) { y1 = rep(y1, n); n4 = n }

if(! (n1 == n2 && n2 == n3 && n3 == n4) ) {
stop_wrap("x0, y0, x1, y1 should have same length.")
}

if(!is.matrix(x0)) x0 = matrix(x0, ncol = 1)
if(!is.matrix(x1)) x1 = matrix(x1, ncol = 1)

if(length(col) == 1) col = rep(col, n)
if(length(border) == 1) border = rep(border, n)
if(length(lwd) == 1) lwd = rep(lwd, n)
if(length(lty) == 1) lty = rep(lty, n)


if(ncol(x0) == 1 && ncol(x1) == 1) {
if(type == "normal") {
circos.segments(x0, y0, x1, y1, sector.index = sector.index, track.index = track.index,
col = col, lwd = lwd, lty = lty, ...)
} else if(type == "segments") {
if(length(segments.ratio) == 1) segments.ratio = rep(segments.ratio, 3)
segments.ratio = segments.ratio[1:3]
segments.ratio = segments.ratio/sum(segments.ratio)
for(i in 1:n) {
w = x1[i] - x0[i]
h = y1[i] - y0[i]
circos.segments(x0[i], y0[i], x0[i], y0[i] + h*segments.ratio[1], col = col[i], lwd = lwd[i], lty = lty[i], straight = TRUE,
sector.index = sector.index, track.index = track.index)
circos.segments(x0[i], y0[i]+h*segments.ratio[1], x1[i], y0[i] + h*sum(segments.ratio[1:2]), col = col[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
circos.segments(x1[i], y0[i]+h*sum(segments.ratio[1:2]), x1[i], y1[i], col = col[i], lwd = lwd[i], lty = lty[i], straight = TRUE,
sector.index = sector.index, track.index = track.index)
}
} else if(type == "bezier") {
for(i in 1:n) {
pt = get_bezier_points(x0[i], y0[i], x1[i], y1[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
circos.lines(pt[, 1], pt[, 2], col = col[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
}
}
} else {
if(type == "segments") {
stop_wrap("'segments' is only allowed for connections as lines where `x0` and `x1` are both set as vectors.")
}

if(type == "normal") {
for(i in 1:n) {
if(ncol(x0) == 2 && ncol(x1) == 2) {
circos.polygon(c(x0[i, 1], x0[i, 2], x1[i, 2], x1[i, 1], x0[i, 1]),
c(y0[i], y0[i], y1[i], y1[i], y0[i]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
} else if(ncol(x0) == 2 && ncol(x1) == 1) {
circos.polygon(c(x0[i, 1], x0[i, 2], x1[i, 1], x0[i, 1]),
c(y0[i], y0[i], y1[i], y0[i]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
} else if(ncol(x0) == 2 && ncol(x1) == 2) {
circos.polygon(c(x0[i, 1], x1[i, 2], x1[i, 1], x0[i, 1]),
c(y0[i], y1[i], y1[i], y0[i]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
}
}
} else if(type == "bezier") {
for(i in 1:n) {
if(ncol(x0) == 2 && ncol(x1) == 2) {
pt1 = get_bezier_points(x0[i, 2], y0[i], x1[i, 2], y1[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
pt2 = get_bezier_points(x1[i, 1], y1[i], x0[i, 1], y0[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
circos.polygon(c(pt1[, 1], pt2[, 1], pt1[1, 1]),
c(pt1[, 2], pt2[, 2], pt1[1, 2]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
} else if(ncol(x0) == 2 && ncol(x1) == 1) {
pt1 = get_bezier_points(x0[i, 2], y0[i], x1[i, 1], y1[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
pt2 = get_bezier_points(x1[i, 1], y1[i], x0[i, 1], y0[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
circos.polygon(c(pt1[, 1], pt2[, 1], pt1[1, 1]),
c(pt1[, 2], pt2[, 2], pt1[1, 2]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
} else if(ncol(x0) == 2 && ncol(x1) == 2) {
pt1 = get_bezier_points(x0[i, 1], y0[i], x1[i, 2], y1[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
pt2 = get_bezier_points(x1[i, 1], y1[i], x0[i, 1], y0[i],
xlim = get.cell.meta.data("xlim", sector.index = sector.index, track.index = track.index),
ylim = get.cell.meta.data("ylim", sector.index = sector.index, track.index = track.index)
)
circos.polygon(c(pt1[, 1], pt2[, 1], pt1[1, 1]),
c(pt1[, 2], pt2[, 2], pt1[1, 2]),
col = col[i], border = border[i], lwd = lwd[i], lty = lty[i],
sector.index = sector.index, track.index = track.index)
}
}
}
}
}
2 changes: 1 addition & 1 deletion man/arrange_links_evenly.Rd
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Expand Up @@ -33,7 +33,7 @@ circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
circos.text(CELL_META$xcenter, CELL_META$ycenter, CELL_META$sector.index)
})

df2 = arrange_links_evenly(df)
df2 = arrange_links_evenly(df, directional = 1)

for(i in seq_len(nrow(df2))) {
s1 = df$from[i]
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