Using "circlize" package in R, I am trying to add labels for each track. In the example below, I want it to show, "A. Ideogram", "B. Expression", "C: Count" in between sectors after sector Y
, before sector 1
.
library(circlize)
circos.initializeWithIdeogram()
bed = generateRandomBed(nr = 500, fun = function(k) runif(k)*sample(c(-1, 1), k, replace = TRUE))
circos.genomicTrackPlotRegion(bed, ylim = c(-1, 1), panel.fun = function(region, value, ...) {
col = ifelse(value[[1]] > 0, "red", "green")
circos.genomicPoints(region, value, col = col, cex = 0.5, pch = 16)
cell.xlim = get.cell.meta.data("cell.xlim")
for(h in c(-1, -0.5, 0, 0.5, 1)) {
circos.lines(cell.xlim, c(h, h), col = "#00000040")
}
}, track.height = 0.1)
bed = generateRandomBed(nr = 500, fun = function(k) rnorm(k, 0, 50))
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
x = (region[[2]] + region[[1]]) / 2
y = value[[1]]
loess.fit = loess(y ~ x)
loess.predict = predict(loess.fit, x, se = TRUE)
d1 = c(x, rev(x))
d2 = c(loess.predict$fit + loess.predict$se.fit, rev(loess.predict$fit - loess.predict$se.fit))
circos.polygon(d1, d2, col = "#CCCCCC", border = NA)
circos.points(x, y, pch = 16, cex = 0.5)
circos.lines(x, loess.predict$fit)
}, track.height = 0.1)
circos.clear()
Hope this helps you. New lines are commented.
library(circlize)
circos.par(gap.after=3) #Increase gap size
circos.initializeWithIdeogram()
#First label, depending on final plot resolution and gap size you'll have to tune the positions
circos.text(sector.index="chr1",track.index = 1,get.cell.meta.data("cell.xlim")-mean(get.cell.meta.data("cell.xlim"))/2,
get.cell.meta.data("cell.ylim")-max(get.cell.meta.data("cell.ylim"))/2, labels = "A. Ideogram",facing = "clockwise",
niceFacing = TRUE, adj = c(0,0),cex = 0.5)
bed = generateRandomBed(nr = 500, fun = function(k) runif(k)*sample(c(-1, 1), k, replace = TRUE))
circos.genomicTrackPlotRegion(bed, ylim = c(-1, 1), panel.fun = function(region, value, ...) {
col = ifelse(value[[1]] > 0, "red", "green")
circos.genomicPoints(region, value, col = col, cex = 0.5, pch = 16)
cell.xlim = get.cell.meta.data("cell.xlim")
for(h in c(-1, -0.5, 0, 0.5, 1)) {
circos.lines(cell.xlim, c(h, h), col = "#00000040")
}
}, track.height = 0.1)
#Second label, depending on final plot resolution and gap size you'll have to tune the positions
circos.text(sector.index="chr1",track.index = 2,get.cell.meta.data("cell.xlim")-mean(get.cell.meta.data("cell.xlim"))/2,
get.cell.meta.data("cell.ylim")-2*max(get.cell.meta.data("cell.ylim")), labels = "B. Expression",facing = "clockwise",
niceFacing = TRUE, adj = c(0,0),cex=0.5)
bed = generateRandomBed(nr = 500, fun = function(k) rnorm(k, 0, 50))
circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
x = (region[[2]] + region[[1]]) / 2
y = value[[1]]
loess.fit = loess(y ~ x)
loess.predict = predict(loess.fit, x, se = TRUE)
d1 = c(x, rev(x))
d2 = c(loess.predict$fit + loess.predict$se.fit, rev(loess.predict$fit - loess.predict$se.fit))
circos.polygon(d1, d2, col = "#CCCCCC", border = NA)
circos.points(x, y, pch = 16, cex = 0.5)
circos.lines(x, loess.predict$fit)
}, track.height = 0.1)
#Thrid label, depending on final plot resolution and gap size you'll have to tune the positions
circos.text(sector.index="chr1",track.index = 4,get.cell.meta.data("cell.xlim")-mean(get.cell.meta.data("cell.xlim"))/2,
get.cell.meta.data("cell.ylim"), labels = "C. Count",facing = "clockwise", niceFacing = TRUE, adj = c(0,0),cex=0.5)
circos.clear()
Result is as follow
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