How do you add track label in R Circlize?

Question

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()

Disclamation

could you show what the expected output is? I don't see where exactly the legend should be, as there seems to be no room in between Y and 1 – Nanosecond

@Cath, yes there is not any, and for now, storm's solution works after I play to create the gaps. Thanks – Disclamation

Answer 1

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

Hygro

Thanks @storm for the answer. Seems to work. I am surprised It is unnecessarily complex, may be developer can add some simple functions. – Disclamation