调整R中的highlight.sector()宽度和位置-弦图(圆环包)

Question

我需要一些帮助调整突出显示的扇区的chordDiagram()从圆圈包。

我正在处理渔业登陆数据。渔船在一个港口(国内港口PORT_DE)开始他们的旅行，在另一个港口(登陆港口PORT_LA)降落他们的渔获物。我的工作是扇贝活重吨(登陆SCALLOP_W)。下面是一个简单的dataframe示例：

        PORT_DE  PORT_LA SCALLOP_W
1      Aberdeen Aberdeen       116
2        Barrow   Barrow        98
3       Douglas   Barrow       127
4 Kirkcudbright   Barrow       113
5       Brixham  Brixham        69
6        Buckie   Buckie       180

每个端口(Name_short)按区域(Region_lb)和国家(Country_lb)标记。下面的例子。

   Name_short Country_lb      Region_lb
1   Scalloway   Scotland Shetland Isles
2   Scrabster   Scotland    North Coast
3      Buckie   Scotland    Moray Firth
4 Fraserburgh   Scotland    Moray Firth
5    Aberdeen   Scotland     North East

使用circilze包，我生成了一个定制的chordDiagram来可视化港口之间的着陆流。我调整了大部分的设置，包括同一国家的港口分组，通过调整扇区之间的间隔(参见gap.after设置)。这是我现在的和弦图，

​

​

我几乎制作了我想要的东西，除了按国家强调行业的最后一点。我试图使用highlight.sector()来突出显示同一个国家的端口，但是我不能调整突出显示扇区的宽度或位置。目前，国家部门与所有其他标签重叠。例子如下：

​

​

请注意，这两个数字之间有不同的颜色，因为颜色是随机生成的。

你能帮我做最后的调整吗？

产生下列数字的代码：

# calculate gaps by country; 
# 1 degree between ports, 10 degree between countries
gaps <- rep(1, nrow(port_coords))
gaps[cumsum(as.numeric(tapply(port_coords$Name_short, port_coords$Country_lb, length)))] <- 10

# edit initialising parameters
circos.par(canvas.ylim=c(-1.5,1.5), # edit  canvas size 
           gap.after = gaps, # adjust gaps between regions
           track.margin = c(0.01, 0)) # adjust bottom and top margin 
                                      # (blank area out of the plotting regio)

# Plot chord diagram
chordDiagram(m,

             # manual order of sectors
             order = port_coords$Name_short,

             # plot only grid (no labels, no axis)
             annotationTrack = "grid", 
             preAllocateTracks = 1, 

             # adjust grid width and spacing
             annotationTrackHeight = c(0.03, 0.01), 

             # add directionality
             directional=1, 
             direction.type = c("diffHeight", "arrows"), 
             link.arr.type = "big.arrow",

             # adjust the starting end of the link
             diffHeight = -uh(1, "mm"),

             # adjust height of all links
             h.ratio = 0.8,

             # add link border
             link.lwd = 1, link.lty = 1, link.border="gray35"

             )

# add labels and axis manually
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")

  # print labels & text size (cex)
  circos.text(mean(xlim), ylim[1] + .7, sector.name, 
              facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.6)

  # print axis
  circos.axis(h = "top", labels.cex = 0.5, major.tick.percentage = 0.2, 
              sector.index = sector.name, track.index = 2)
}, bg.border = NA)

# add additional track to enhance the visual effect of different groups
# Scotland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Scotland")],
                 track.index = 1, col = "blue",
                 text = "Scotland", cex = 0.8, text.col = "white", niceFacing = TRUE)
# England
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "England")],
                 track.index = 1, col = "red",
                 text = "England", cex = 0.8, text.col = "white", niceFacing = TRUE)
# Wales
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Wales")],
                 track.index = 1, col = "forestgreen",
                 text = "Wales", cex = 0.8, text.col = "white", niceFacing = TRUE)
# Isle of Man
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Isle of Man")],
                 track.index = 1, col = "darkred",
                 text = "Isle of Man", cex = 0.8, text.col = "white", niceFacing = TRUE)
# Rep. Ireland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Rep. Ireland")],
                 track.index = 1, col = "darkorange2",
                 text = "Ireland", cex = 0.8, text.col = "white", niceFacing = TRUE)
# N.Ireland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "N.Ireland")],
                 track.index = 1, col = "magenta4",
                 text = "N. Ireland", cex = 0.8, text.col = "white", niceFacing = TRUE)

# re-set circos parameters
circos.clear()

Answer 1

我已经尝试了一段时间来寻找解决方案。现在，我已经通过调整默认的轨道边距和默认的轨道高度来调整highlight.sector()的位置和宽度。

我在初始化track.margin步骤时指定了track.height和circos.par()参数。

最终产品如下所示。在答案的结尾处编码。

​

​

# calculate gaps by country; 
# 1 degree between ports, 10 degree between countries
gaps <- rep(1, nrow(port_coords))
gaps[cumsum(as.numeric(tapply(port_coords$Name_short, port_coords$Country_lb, length)))] <- 10

# edit initialising parameters
circos.par(canvas.ylim=c(-1.5,1.5), # edit  canvas size 
           gap.after = gaps, # adjust gaps between regions
           track.margin = c(0.01, 0.05), # adjust bottom and top margin
           # track.margin = c(0.01, 0.1)
           track.height = 0.05)

# Plot chord diagram
chordDiagram(m,

             # manual order of sectors
             order = port_coords$Name_short,

             # plot only grid (no labels, no axis)
             annotationTrack = "grid",
             # annotationTrack = NULL, 
             preAllocateTracks = 1, 

             # adjust grid width and spacing
             annotationTrackHeight = c(0.03, 0.01), 

             # add directionality
             directional=1, 
             direction.type = c("diffHeight", "arrows"), 
             link.arr.type = "big.arrow",

             # adjust the starting end of the link
             diffHeight = -uh(1, "mm"),

             # adjust height of all links
             h.ratio = 0.8,

             # add link border
             link.lwd = 1, link.lty = 1, link.border="gray35"

             # track.margin = c(0.01, 0.1)

             )

# Scotland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Scotland")],
                 track.index = 1, col = "blue2",
                 text = "Scotland", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)
# England
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "England")],
                 track.index = 1, col = "red2",
                 text = "England", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)
# Wales
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Wales")],
                 track.index = 1, col = "springgreen4",
                 text = "Wales", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)
# Isle of Man
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Isle of Man")],
                 track.index = 1, col = "orangered4",
                 text = "Isle of Man", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)
# Rep. Ireland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "Rep. Ireland")],
                 track.index = 1, col = "darkorange3",
                 text = "Ireland", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)
# N.Ireland
highlight.sector(port_coords$Name_short[which(port_coords$Country_lb == "N.Ireland")],
                 track.index = 1, col = "magenta4",
                 text = "NI", cex = 1, text.col = "white", 
                 niceFacing = TRUE, font=2)

# add labels and axis manually
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")

  # print labels & text size (cex)
  # circos.text(mean(xlim), ylim[1] + .7, sector.name, 
  #             facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.6)

  circos.text(mean(xlim), ylim[1] + 2, sector.name, 
              facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.6)

  # print axis
  circos.axis(h = "bottom", labels.cex = 0.5, 
              # major.tick.percentage = 0.05, 
              major.tick.length = 0.6,
              sector.index = sector.name, track.index = 2)
}, bg.border = NA)

# re-set circos parameters
circos.clear()

Answer 2

如果你像我一样有点强迫症，你也可以把sector.numeric.index添加到扇区，并在旁边添加一个传奇，所以它看起来只是有点像这，只是我的2分钱！