从 circlize 包中对齐 chordDiagram 中的标签

Question

我有一个相当复杂的 circos 图并且在对齐标签时遇到了一些问题。

为了演示这个问题，我在下面提供了一个简短的可重现示例。

我不知道如何很好地对齐每个标签，使它们与相应的段的距离完全相同，例如根据霸王龙标签。许多标签是隐藏和重叠的，并且与绘图边缘的距离不同。任何帮助将不胜感激。

library("circlize")
circos.clear()

# create data
somelongnames <- c("homo sapiens", "arabidopsis thaliania", "Tyrannosaurus rex",
                  "some other long name", letters[seq(4)])

df <- data.frame(x = somelongnames,
                 y = c("this label is very far away from the plot", "Golgi", 
                       letters[13:18]),
                 count = c(2, 10, 4, 5, 5, 1, 9, 3))

# set colours
ll <- unique(c(df$x, df$y))
grid.col <- rainbow(length(ll))
grid.col <- setNames(grid.col, ll)

# create plot
par(mar = c(1,1,1,1)*12, cex = 0.6, xpd=NA)

chordDiagram(df, annotationTrack = "grid", 
             preAllocateTracks = 1, 
             grid.col = grid.col,
             directional = 1, 
             direction.type = c("diffHeight", "arrows"), 
             link.arr.type = "big.arrow")

circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.name = get.cell.meta.data("sector.index")
  circos.text(mean(xlim), 
              ylim[1] + .1, 
              sector.name, 
              facing = "clockwise",
              niceFacing = TRUE, 
              adj = c(-0.5, 0.1),
              cex = 1,
              col=grid.col[sector.name],
              font = 2)
  circos.axis(h = "top",
              labels.cex = .6,
              major.tick.length = 1,
              sector.index = sector.name,
              track.index = 2)
}, bg.border = NA)

Answer 1

这个问题已经answered here by the package author of circlize

在此重新发帖回答以上问题-

主要问题是circos.axis()中track.index = 2的设置改变了当前曲目。

将 y 轴上的位置更改为 ylim[1] + cm_h(2)。这意味着 y = ylim[1] 偏移了 2cm。（图上好像不是真的2cm，但是你可以手动改变这个值）。 adj 更改为 adj = c(0, 0.5)。请注意 adj 的值乘以文本长度，因此所有扇区名称的物理长度都不相同。删除 major.tick.length = 1 因为我认为刻度的默认长度应该没问题。

下面的代码解决了上面的问题

chordDiagram(df, annotationTrack = "grid", 
             preAllocateTracks = 1, 
             grid.col = grid.col,
             directional = 1, 
             direction.type = c("diffHeight", "arrows"), 
             link.arr.type = "big.arrow")

circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.name = get.cell.meta.data("sector.index")
  circos.text(CELL_META$xcenter, 
              ylim[1] + cm_h(2), 
              sector.name, 
              facing = "clockwise",
              niceFacing = TRUE, 
              adj = c(0, 0.5),
              cex = 1,
              col=grid.col[sector.name],
              font = 2)
  circos.axis(h = "bottom",
              labels.cex = .6,
              sector.index = sector.name
              )
}, bg.border = NA)

从 circlize 包中对齐 chordDiagram 中的标签

Aligning labels in a chordDiagram from circlize package

r

chord-diagram

circlize