问题
I need some help with adjusting highlighted sectors of a chordDiagram() from the circlize package.
I am working with fisheries landings data. Fishing vessels start their trip in one port (homeport PORT_DE), and land their catch in another port (landing port PORT_LA). I am working with scallops live weight in tonnes (landings SCALLOP_W). Here is a simple example of the dataframe:
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
Each port (Name_short) is labeled by region (Region_lb), and by country (Country_lb). Example below.
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
Using the circilze package, I have generated a customised chordDiagram to visualise the flow of landings between ports. I have adjusted most of the settings, including grouping of ports of the same nation, by adjusting the spacing between sectors (see gap.after setting). This is the current form of my chord diagram,
I have nearly produced what I want, apart from the final touch of highlighting sectors by country. I am trying to use highlight.sector() in order to highlight ports of the same country, but I cannot adjust either the width or the placement of the highlighted sector. Currently, the country sectors overlap with all the other labels. Example below:
Please note that there are different colours between the two figures as colours are randomly generated.
Could you please assist me with the final adjustments?
Code for producing the figures shown below:
# 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$Country_lb == "N.Ireland")],
track.index = 1, col = "magenta4",
text = "N. Ireland", cex = 0.8, text.col = "white", niceFacing = TRUE)
# re-set circos parameters
circos.clear()
回答1:
I have been trying for a while now to find a solution. I have now managed to adjust the placement and the width of the highlight.sector() by adjusting the default track margins and default track height.
I have done so by specifying track.margin and track.height parameters in the initialisation of circos.par() step.
The end product looks like below. Code at the end the answer.
# calculate gaps by country;
# 1 degree between ports, 10 degree between countries
gaps <- rep(1, nrow(port_coords))
gaps[cumsum(as.numeric(tapply(port_coords$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()
回答2:
If you're a little ocd like myself, you could also add the sector.numeric.index into the sectors and add a legend on the side, so it looks just a tad better like this, just my 2 cents!
来源：https://stackoverflow.com/questions/48723254/adjust-highlight-sector-width-and-placement-chord-diagram-circlize-package