Как добавить метку трека в R Circlize? - PullRequest
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Как добавить метку трека в R Circlize?

0 голосов
/ 03 декабря 2018

Используя пакет "circlize" в R, я пытаюсь добавить метки для каждого трека.В приведенном ниже примере я хочу, чтобы он показывал «A. Идеограмма», «B. Выражение», «C: Count» между секторами после сектора Y, перед сектором 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()

enter image description here

1 Ответ

0 голосов
/ 07 декабря 2018

Надеюсь, это поможет вам.Новые строки комментируются.

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()

Результат выглядит следующим образом

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