R/circos.nested.R
In jokergoo/circlize: Circular Visualization
Defines functions
strwrap2
circos.nested
Documented in
circos.nested
# == title
# Nested zooming with two circular plots
#
# == param
# -f1 A self-defined function for making the first circular plot. The function should have no argument.
# -f2 A self-defined function for making the second circular plot. The function should have no argument.
# -correspondance A six-column data frame which contains correspondance between the
# coordinates in two circular plots
# -connection_height The height of the connection track, measured as the percent to the radius of the unit circle.
# The value can be specified by `uh` or `convert_height` with absolute units.
# -connection_col Filled color of the connection track. The value can be a vector with same length as number of rows of ``correspondance``
# -connection_border Border color of the connection track.
# -connection_lty Line style of the connection track borders
# -connection_lwd Line width of the connection track borders
# -adjust_start_degree If ``circos.par(start.degree = ...)`` is not set in ``f2()``, the start degree for the second
# circular plot will be adjusted to make the distance of sectors between the two plots to the minimal.
#
# == details
# The function visualizes zoomings by combining two circular plots into one page where
# one is the normal circular plot and the other one only contains regions that need to be zoomed.
# This function automatically arranges the two plots to make it easy to correspond between
# the original and the zoomed sectors.
#
# Since the function needs to know the information of the two circular plots, please do not call
# `circos.clear` in either ``f1()`` or ``f2()``. It will be called internally in `circos.nested`.
#
# If ``adjust_start_degree`` is set to ``TRUE``, ``start.degree`` should not be set in ``f2()``.
# Also ``canvas.xlim`` and ``canvas.ylim`` are reset in ``f2()``, they should not be set in ``f2()``
# either.
#
# == seealso
# https://jokergoo.github.io/circlize_book/book/nested-zooming.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
circos.nested = function(
f1,
f2,
correspondance,
connection_height = mm_h(5),
connection_col = NA,
connection_border = "black",
connection_lty = par("lty"),
connection_lwd = par("lwd"),
adjust_start_degree = TRUE) {
on.exit(circos.clear())
nr = nrow(correspondance)
od = order(correspondance[, 2], correspondance[, 3], correspondance[, 5], correspondance[, 6])
correspondance = correspondance[od, ]
if(length(connection_col) == 1) connection_col = rep(connection_col, nr)
if(length(connection_border) == 1) connection_border = rep(connection_border, nr)
if(length(connection_lty) == 1) connection_lty = rep(connection_lty, nr)
if(length(connection_lwd) == 1) connection_lwd = rep(connection_lwd, nr)
connection_col = connection_col[od]
connection_border = connection_border[od]
connection_lty = connection_lty[od]
connection_lwd = connection_lwd[od]
pdf(NULL)
oe = try({
f2()
if(!is.circos.initialized()) {
stop_wrap("Do not call `circos.clear()` in `f2`.")
}
param2 = circos.par()
correspondance[[1]] = as.vector(correspondance[[1]])
correspondance[[4]] = as.vector(correspondance[[4]])
all_sn = get.all.sector.index()
l = correspondance[[4]] %in% all_sn
correspondance = correspondance[l, , drop = FALSE]
if(nrow(correspondance) == 0) {
stop_wrap("Cannot map `correspondance` (the fourth column) to sectors in `f2()`.")
}
if(length(connection_col) > 1) connection_col = connection_col[l]
if(length(connection_border) > 1) connection_border = connection_border[l]
if(length(connection_lty) > 1) connection_lty = connection_lty[l]
if(length(connection_lwd) > 1) connection_lwd = connection_lwd[l]
for(i in seq_len(nrow(correspondance))) {
correspondance[i, "c2_theta1"] = circlize(correspondance[i, 5], 1, sector.index = correspondance[i, 4])[1, 1]
correspondance[i, "c2_theta2"] = circlize(correspondance[i, 6], 1, sector.index = correspondance[i, 4])[1, 1]
}
if(!identical(c(-1, 1), param2$canvas.xlim)) {
stop_wrap("Do not modify circos.par('canvas.xlim') in `f2()`.")
}
if(!identical(c(-1, 1), param2$canvas.ylim)) {
stop_wrap("Do not modify circos.par('canvas.ylim') in `f2()`.")
}
if(adjust_start_degree) {
if(!identical(0, param2$start.degree)) {
stop_wrap("Do not modify circos.par('start.degree') when adjust_start_degree = TRUE in `f2()`.")
}
}
f2_sectors = all_sn
correspondance$c2_order = order(factor(correspondance[, 4], levels = f2_sectors), correspondance[, 5], correspondance[, 6])
})
circos.clear()
dev.off2()
if(inherits(oe, "try-error")) {
stop(oe)
}
# in correspondace, positions are already sorted by the 4,5,6 columns
# here we test for a sector in f1(),
# if(any(tapply(correspondance[, 2], correspondance[, 1], is.unsorted))) {
# warning(strwrap2("Sectors in `f2()` which belongs to one single sector in `f1()` should be sorted by positions, or else connection lines may overlap."))
# }
# if(!all(tapply(seq_len(nrow(correspondance)), correspondance[, 1], function(x) {
# if(length(x) == 1) {
# TRUE
# } else {
# all(diff(x) == 1)
# }
# }))) {
# warning(strwrap2("Sectors in `f2()` should be sorted by the sector order in `f1()`, or else connection lines may overlap."))
# }
circos.par(points.overflow.warning = FALSE)
f1()
if(!is.circos.initialized()) {
stop_wrap("Do not call `circos.clear()` in `f1`.")
}
param1 = circos.par()
if(abs(abs(param1$canvas.xlim[1]) - abs(param1$canvas.xlim[2])) > 1e-6) {
stop_wrap("`canvas.xlim` should be symmetric to zero in `f1()`.")
}
if(abs(abs(param1$canvas.ylim[1]) - abs(param1$canvas.ylim[2])) > 1e-6) {
stop_wrap("`canvas.ylim` should be symmetric to zero in `f1()`.")
}
if(abs(abs(param1$canvas.xlim[1]) - abs(param1$canvas.ylim[1])) > 1e-6) {
stop_wrap("Canvas coordinate should be square in `f1()`.")
}
all_sn = get.all.sector.index()
l = correspondance[[1]] %in% all_sn
correspondance = correspondance[l, , drop = FALSE]
if(nrow(correspondance) == 0) {
stop_wrap("Cannot map `correspondance` (the first column) to sectors in `f1()`.")
}
if(length(connection_col) > 1) connection_col = connection_col[l]
if(length(connection_border) > 1) connection_border = connection_border[l]
if(length(connection_lty) > 1) connection_lty = connection_lty[l]
if(length(connection_lwd) > 1) connection_lwd = connection_lwd[l]
for(i in seq_len(nrow(correspondance))) {
correspondance[i, "c1_theta1"] = circlize(correspondance[i, 2], 1, sector.index = correspondance[i, 1])[1, 1]
correspondance[i, "c1_theta2"] = circlize(correspondance[i, 3], 1, sector.index = correspondance[i, 1])[1, 1]
}
r1 = get_most_inside_radius()
r2 = r1 - connection_height
f1_sectors = all_sn
correspondance$c1_order = order(factor(correspondance[, 1], levels = f1_sectors), correspondance[, 2], correspondance[, 3])
## adjust start degree of the second circular plot
if(adjust_start_degree) {
t1 = rowMeans(correspondance[, c("c2_theta1", "c2_theta2")])
t2 = rowMeans(correspondance[, c("c1_theta1", "c1_theta2")])
sum_diff = numeric(360)
for(offset in 0:359) {
diff_degree = abs(t1 - t2 + offset)
diff_degree = ifelse(diff_degree > 180, diff_degree - 180, diff_degree)
sum_diff[offset + 1] = sum(diff_degree)
}
offset = which.min(sum_diff) - 1
correspondance[, "c2_theta1"] = correspondance[, "c2_theta1"] + offset
correspondance[, "c2_theta2"] = correspondance[, "c2_theta2"] + offset
}
# the coordinate convert is applied in the first circular plot
# connection is from the top to the bottom of this track
make_connection = function(chr, c1_theta1, c1_theta2, c2_theta1, c2_theta2,
col, border, lty, lwd) {
cell.top.radius = get.cell.meta.data("cell.top.radius")
cell.bottom.radius = get.cell.meta.data("cell.bottom.radius")
df = reverse.circlize(c(c1_theta1, c1_theta2, c2_theta1, c2_theta2),
c(cell.top.radius, cell.top.radius, cell.bottom.radius, cell.bottom.radius))
x21 = df[1, 1]
x22 = df[2, 1]
y21 = df[1, 2]
y22 = df[2, 2]
x11 = df[3, 1]
x12 = df[4, 1]
y11 = df[3, 2]
y12 = df[4, 2]
circos.polygon(c(x11, x11, x21, x21, x22, x22, x12, x12, x11),
c(y11, (y21 - y11)/3, (y21 - y11)/3*2, y21, y22, (y22 - y12)/3*2, (y22 - y12)/3, y12, y11),
col = col, border = border, lty = lty, lwd = lwd)
}
nr = nrow(correspondance)
if(length(connection_col) == 1) {
connection_col = rep(connection_col, nr)
}
if(length(connection_border) == 1) {
connection_border = rep(connection_border, nr)
}
if(length(connection_lty) == 1) {
connection_lty = rep(connection_lty, nr)
}
if(length(connection_lwd) == 1) {
connection_lwd = rep(connection_lwd, nr)
}
# make the connections
circos.track(ylim = c(0, 1), track.height = connection_height, panel.fun = function(x, y) {
l = correspondance[[1]] == CELL_META$sector.index
if(sum(l) == 0) {
return(NULL)
}
for(i in which(l)) {
make_connection(correspondance[i, 1], correspondance[i, "c1_theta1"], correspondance[i, "c1_theta2"],
correspondance[i, "c2_theta1"], correspondance[i, "c2_theta2"],
connection_col[i], connection_border[i], connection_lty[i], connection_lwd[i])
}
}, track.margin = c(0, 0), cell.padding = c(0, 0, 0, 0), bg.border = NA)
circos.clear()
op = par("new")
par(new = TRUE)
if(adjust_start_degree) {
circos.par(start.degree = offset)
}
circos.par(canvas.xlim = c(-param1$canvas.xlim[2]/r2, param1$canvas.xlim[2]/r2),
canvas.ylim = c(-param1$canvas.xlim[2]/r2, param1$canvas.xlim[2]/r2))
f2()
circos.clear()
par(new = op)
if(!all(correspondance$c1_order == correspondance$c2_order)) {
warning_wrap(paste0("Sectors in `f1()` and `f2()` should be in the same order, or else the connection lines may overlap.
The ordered sectors in outter ring: ", paste(f1_sectors, collapse = ', '), ". The ordered sectors in inner
ring: ", paste0(f2_sectors, collapse = ', '), ".\n"))
}
}
dev.off2 = function () {
i1 = dev.prev()
i2 = dev.cur()
if (i1 == 2) {
dev.set(i1)
}
else if (i1 > 2) {
i11 = dev.prev(i1)
if (names(i11) == "RStudioGD") {
dev.set(i11)
}
else {
dev.set(i1)
}
}
dev.off(i2)
}
strwrap2 = function(x) {
paste(strwrap(x), collapse = "\n")
}
jokergoo/circlize documentation built on Nov. 17, 2023, 11:32 a.m.
R Package Documentation
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Defines functions strwrap2 circos.nested
Documented in circos.nested
# == title
# Nested zooming with two circular plots
#
# == param
# -f1 A self-defined function for making the first circular plot. The function should have no argument.
# -f2 A self-defined function for making the second circular plot. The function should have no argument.
# -correspondance A six-column data frame which contains correspondance between the
# coordinates in two circular plots
# -connection_height The height of the connection track, measured as the percent to the radius of the unit circle.
# The value can be specified by `uh` or `convert_height` with absolute units.
# -connection_col Filled color of the connection track. The value can be a vector with same length as number of rows of ``correspondance``
# -connection_border Border color of the connection track.
# -connection_lty Line style of the connection track borders
# -connection_lwd Line width of the connection track borders
# -adjust_start_degree If ``circos.par(start.degree = ...)`` is not set in ``f2()``, the start degree for the second
# circular plot will be adjusted to make the distance of sectors between the two plots to the minimal.
#
# == details
# The function visualizes zoomings by combining two circular plots into one page where
# one is the normal circular plot and the other one only contains regions that need to be zoomed.
# This function automatically arranges the two plots to make it easy to correspond between
# the original and the zoomed sectors.
#
# Since the function needs to know the information of the two circular plots, please do not call
# `circos.clear` in either ``f1()`` or ``f2()``. It will be called internally in `circos.nested`.
#
# If ``adjust_start_degree`` is set to ``TRUE``, ``start.degree`` should not be set in ``f2()``.
# Also ``canvas.xlim`` and ``canvas.ylim`` are reset in ``f2()``, they should not be set in ``f2()``
# either.
#
# == seealso
# https://jokergoo.github.io/circlize_book/book/nested-zooming.html
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
circos.nested = function(
f1,
f2,
correspondance,
connection_height = mm_h(5),
connection_col = NA,
connection_border = "black",
connection_lty = par("lty"),
connection_lwd = par("lwd"),
adjust_start_degree = TRUE) {
on.exit(circos.clear())
nr = nrow(correspondance)
od = order(correspondance[, 2], correspondance[, 3], correspondance[, 5], correspondance[, 6])
correspondance = correspondance[od, ]
if(length(connection_col) == 1) connection_col = rep(connection_col, nr)
if(length(connection_border) == 1) connection_border = rep(connection_border, nr)
if(length(connection_lty) == 1) connection_lty = rep(connection_lty, nr)
if(length(connection_lwd) == 1) connection_lwd = rep(connection_lwd, nr)
connection_col = connection_col[od]
connection_border = connection_border[od]
connection_lty = connection_lty[od]
connection_lwd = connection_lwd[od]
pdf(NULL)
oe = try({
f2()
if(!is.circos.initialized()) {
stop_wrap("Do not call `circos.clear()` in `f2`.")
}
param2 = circos.par()
correspondance[[1]] = as.vector(correspondance[[1]])
correspondance[[4]] = as.vector(correspondance[[4]])
all_sn = get.all.sector.index()
l = correspondance[[4]] %in% all_sn
correspondance = correspondance[l, , drop = FALSE]
if(nrow(correspondance) == 0) {
stop_wrap("Cannot map `correspondance` (the fourth column) to sectors in `f2()`.")
}
if(length(connection_col) > 1) connection_col = connection_col[l]
if(length(connection_border) > 1) connection_border = connection_border[l]
if(length(connection_lty) > 1) connection_lty = connection_lty[l]
if(length(connection_lwd) > 1) connection_lwd = connection_lwd[l]
for(i in seq_len(nrow(correspondance))) {
correspondance[i, "c2_theta1"] = circlize(correspondance[i, 5], 1, sector.index = correspondance[i, 4])[1, 1]
correspondance[i, "c2_theta2"] = circlize(correspondance[i, 6], 1, sector.index = correspondance[i, 4])[1, 1]
}
if(!identical(c(-1, 1), param2$canvas.xlim)) {
stop_wrap("Do not modify circos.par('canvas.xlim') in `f2()`.")
}
if(!identical(c(-1, 1), param2$canvas.ylim)) {
stop_wrap("Do not modify circos.par('canvas.ylim') in `f2()`.")
}
if(adjust_start_degree) {
if(!identical(0, param2$start.degree)) {
stop_wrap("Do not modify circos.par('start.degree') when adjust_start_degree = TRUE in `f2()`.")
}
}
f2_sectors = all_sn
correspondance$c2_order = order(factor(correspondance[, 4], levels = f2_sectors), correspondance[, 5], correspondance[, 6])
})
circos.clear()
dev.off2()
if(inherits(oe, "try-error")) {
stop(oe)
}
# in correspondace, positions are already sorted by the 4,5,6 columns
# here we test for a sector in f1(),
# if(any(tapply(correspondance[, 2], correspondance[, 1], is.unsorted))) {
# warning(strwrap2("Sectors in `f2()` which belongs to one single sector in `f1()` should be sorted by positions, or else connection lines may overlap."))
# }
# if(!all(tapply(seq_len(nrow(correspondance)), correspondance[, 1], function(x) {
# if(length(x) == 1) {
# TRUE
# } else {
# all(diff(x) == 1)
# }
# }))) {
# warning(strwrap2("Sectors in `f2()` should be sorted by the sector order in `f1()`, or else connection lines may overlap."))
# }
circos.par(points.overflow.warning = FALSE)
f1()
if(!is.circos.initialized()) {
stop_wrap("Do not call `circos.clear()` in `f1`.")
}
param1 = circos.par()
if(abs(abs(param1$canvas.xlim[1]) - abs(param1$canvas.xlim[2])) > 1e-6) {
stop_wrap("`canvas.xlim` should be symmetric to zero in `f1()`.")
}
if(abs(abs(param1$canvas.ylim[1]) - abs(param1$canvas.ylim[2])) > 1e-6) {
stop_wrap("`canvas.ylim` should be symmetric to zero in `f1()`.")
}
if(abs(abs(param1$canvas.xlim[1]) - abs(param1$canvas.ylim[1])) > 1e-6) {
stop_wrap("Canvas coordinate should be square in `f1()`.")
}
all_sn = get.all.sector.index()
l = correspondance[[1]] %in% all_sn
correspondance = correspondance[l, , drop = FALSE]
if(nrow(correspondance) == 0) {
stop_wrap("Cannot map `correspondance` (the first column) to sectors in `f1()`.")
}
if(length(connection_col) > 1) connection_col = connection_col[l]
if(length(connection_border) > 1) connection_border = connection_border[l]
if(length(connection_lty) > 1) connection_lty = connection_lty[l]
if(length(connection_lwd) > 1) connection_lwd = connection_lwd[l]
for(i in seq_len(nrow(correspondance))) {
correspondance[i, "c1_theta1"] = circlize(correspondance[i, 2], 1, sector.index = correspondance[i, 1])[1, 1]
correspondance[i, "c1_theta2"] = circlize(correspondance[i, 3], 1, sector.index = correspondance[i, 1])[1, 1]
}
r1 = get_most_inside_radius()
r2 = r1 - connection_height
f1_sectors = all_sn
correspondance$c1_order = order(factor(correspondance[, 1], levels = f1_sectors), correspondance[, 2], correspondance[, 3])
## adjust start degree of the second circular plot
if(adjust_start_degree) {
t1 = rowMeans(correspondance[, c("c2_theta1", "c2_theta2")])
t2 = rowMeans(correspondance[, c("c1_theta1", "c1_theta2")])
sum_diff = numeric(360)
for(offset in 0:359) {
diff_degree = abs(t1 - t2 + offset)
diff_degree = ifelse(diff_degree > 180, diff_degree - 180, diff_degree)
sum_diff[offset + 1] = sum(diff_degree)
}
offset = which.min(sum_diff) - 1
correspondance[, "c2_theta1"] = correspondance[, "c2_theta1"] + offset
correspondance[, "c2_theta2"] = correspondance[, "c2_theta2"] + offset
}
# the coordinate convert is applied in the first circular plot
# connection is from the top to the bottom of this track
make_connection = function(chr, c1_theta1, c1_theta2, c2_theta1, c2_theta2,
col, border, lty, lwd) {
cell.top.radius = get.cell.meta.data("cell.top.radius")
cell.bottom.radius = get.cell.meta.data("cell.bottom.radius")
df = reverse.circlize(c(c1_theta1, c1_theta2, c2_theta1, c2_theta2),
c(cell.top.radius, cell.top.radius, cell.bottom.radius, cell.bottom.radius))
x21 = df[1, 1]
x22 = df[2, 1]
y21 = df[1, 2]
y22 = df[2, 2]
x11 = df[3, 1]
x12 = df[4, 1]
y11 = df[3, 2]
y12 = df[4, 2]
circos.polygon(c(x11, x11, x21, x21, x22, x22, x12, x12, x11),
c(y11, (y21 - y11)/3, (y21 - y11)/3*2, y21, y22, (y22 - y12)/3*2, (y22 - y12)/3, y12, y11),
col = col, border = border, lty = lty, lwd = lwd)
}
nr = nrow(correspondance)
if(length(connection_col) == 1) {
connection_col = rep(connection_col, nr)
}
if(length(connection_border) == 1) {
connection_border = rep(connection_border, nr)
}
if(length(connection_lty) == 1) {
connection_lty = rep(connection_lty, nr)
}
if(length(connection_lwd) == 1) {
connection_lwd = rep(connection_lwd, nr)
}
# make the connections
circos.track(ylim = c(0, 1), track.height = connection_height, panel.fun = function(x, y) {
l = correspondance[[1]] == CELL_META$sector.index
if(sum(l) == 0) {
return(NULL)
}
for(i in which(l)) {
make_connection(correspondance[i, 1], correspondance[i, "c1_theta1"], correspondance[i, "c1_theta2"],
correspondance[i, "c2_theta1"], correspondance[i, "c2_theta2"],
connection_col[i], connection_border[i], connection_lty[i], connection_lwd[i])
}
}, track.margin = c(0, 0), cell.padding = c(0, 0, 0, 0), bg.border = NA)
circos.clear()
op = par("new")
par(new = TRUE)
if(adjust_start_degree) {
circos.par(start.degree = offset)
}
circos.par(canvas.xlim = c(-param1$canvas.xlim[2]/r2, param1$canvas.xlim[2]/r2),
canvas.ylim = c(-param1$canvas.xlim[2]/r2, param1$canvas.xlim[2]/r2))
f2()
circos.clear()
par(new = op)
if(!all(correspondance$c1_order == correspondance$c2_order)) {
warning_wrap(paste0("Sectors in `f1()` and `f2()` should be in the same order, or else the connection lines may overlap.
The ordered sectors in outter ring: ", paste(f1_sectors, collapse = ', '), ". The ordered sectors in inner
ring: ", paste0(f2_sectors, collapse = ', '), ".\n"))
}
}
dev.off2 = function () {
i1 = dev.prev()
i2 = dev.cur()
if (i1 == 2) {
dev.set(i1)
}
else if (i1 > 2) {
i11 = dev.prev(i1)
if (names(i11) == "RStudioGD") {
dev.set(i11)
}
else {
dev.set(i1)
}
}
dev.off(i2)
}
strwrap2 = function(x) {
paste(strwrap(x), collapse = "\n")
}
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