从circlize包中对齐chordDiagram中的标签

Question

我有一个相当复杂的circos图，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的示例。

我想不出如何很好地对齐每个标签，使它们与相应片段的距离完全相同，例如，根据标签tyranosauras rex。许多标签都是隐藏和重叠的，并且与绘图边缘的距离不同。任何帮助都将不胜感激。

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了

在这里重新发布，以回答上述问题-

主要的问题是circos.axis()中track.index = 2的设置改变了当前的曲目。

将y轴上的位置更改为ylim[1] + cm_h(2)。这意味着y = ylim[1]的偏移量为2 2cm。(在绘图上看起来并不是真正的2厘米，但您可以手动更改此值)。adj更改为adj = c(0, 0.5)。请注意，adj的值乘以文本长度的长度，因此所有扇区名称的物理长度都不相同。删除major.tick.length = 1，因为我认为记号的默认长度看起来应该没问题。

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)

​

​