論文
A latitudinal gradient of deep-sea invasions for marine fishes
https://www.nature.com/articles/s41467-023-36501-4
s41467-023-36501-4.pdf
論文中對應的圖實現的代碼都有,鏈接是
https://github.com/stfriedman/Depth-transitions-paper
裏面有個弦圖很好看,在論文中對應的是figure3, 對應畫圖代碼是上面鏈接中的figure2
論文中的作圖數據是沒有提供的,這裏我就隨便構造一個數據,能夠把論文中提供的代碼運行通就可以
示例數據集
讀取數據集
library(readxl)
dat<-read_excel("data/20230301/20230301.xlsx")
dat
作圖代碼
circos.clear()
circos.par(start.degree = 90,
#gap.degree = 4,
points.overflow.warning = FALSE,
gap.after=c("A1"=5,"A2"=5,"A3"=15,
"B1"=5,"B2"=5,"B3"=15,
"D1"=5,"D2"=5,"D3"=15))
grid.col<-c("A1"="#B0E0E6","A2"="#2C8EB5","A3"="#16465B",
"B1"="#B0E0E6","B2"="#2C8EB5","B3"="#16465B",
"D1"="#B0E0E6","D2"="#2C8EB5","D3"="#16465B")
group<-c("A1"="A","A2"="A","A3"="A",
"B1"="B","B2"="B","B3"="B",
"D1"="D","D2"="D","D3"="D")
chordDiagram(dat,
grid.col = grid.col,
col = rand_color(nrow(dat)),
group = group,
transparency = 0.25,
directional = 1,
direction.type = c("arrows", "diffHeight"),
diffHeight = -0.04,
annotationTrack = "grid",
annotationTrackHeight = c(0.08, 0.1),
link.arr.type = "big.arrow",
# link.sort = TRUE,
# link.decreasing = TRUE,
link.largest.ontop = TRUE,
preAllocateTracks = list(
track.height = 0.1,
track.margin = c(0.01, 0)
))
circos.trackPlotRegion(
track.index = 2,
bg.border = NA,
panel.fun = function(x, y) {
xlim = get.cell.meta.data("xlim")
#sector.index = get.cell.meta.data("sector.index")
sector.index = gsub("[a-z]+_", "", get.cell.meta.data("sector.index"))
# Add names to the sector.
circos.text(
x = mean(xlim),
y = 0.5,
col = "white",
labels = sector.index,
facing = "bending",
cex = 1,
niceFacing = TRUE
)
}
)
names(group[7:9])
i<-1
highlight.sector(names(group[7:9]), track.index = 1, facing = "bending", font = 2,
col = ifelse(i == 1, "#E6AE48FF", "#E6AE483a"),
border = ifelse(i == 1, TRUE, FALSE),
lwd = ifelse(i == 1, 2, 0.01),
text = "tropical", cex = 1.5, text.col = "white", niceFacing = TRUE)
highlight.sector(names(group[4:6]), track.index = 1, facing = "bending", font = 2,
border = ifelse(i == 2, TRUE, FALSE),
lwd = ifelse(i == 2, 2, 0.01),
col = ifelse(i == 2, "#20A486", "#20A4863a"),
text = "temperate", cex = 1.5, text.col = "white", niceFacing = TRUE)
highlight.sector(names(group[1:3]), track.index = 1, facing = "bending", font = 2,
col = ifelse(i == 3, "#472D7B", "#472D7B3a"),
border = ifelse(i == 3, TRUE, FALSE),
lwd = ifelse(i == 3, 2, 0.01),
text = "polar", cex = 1.5, text.col = "white", niceFacing = TRUE)
}
代碼裏有很多參數,這裏有的我也不太清楚是用來做什麼的,先記錄實現代碼,後續如果有需求做這個圖,再來研究具體參數的意思
https://jokergoo.github.io/circlize_book/book/the-chorddiagram-function.html 做這個圖可以參考這個鏈接
示例數據和代碼可以給推文點贊,然後點擊在看,最後留言獲取
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