首页 > 随笔 > 跟着Nature Communications学作图：R语言circlize包做漂亮的弦图

跟着Nature Communications学作图：R语言circlize包做漂亮的弦图

简书 2023-03-01 20:31 1 阅读查看原文

数据可视化 R语言学术论文

论文

A latitudinal gradient of deep-sea invasions for marine fishes

https://www.nature.com/articles/s41467-023-36501-4

s41467-023-36501-4.pdf

论文中对应的图实现的代码都有，链接是

https://github.com/stfriedman/Depth-transitions-paper

里面有个弦图很好看，在论文中对应的是figure3, 对应画图代码是上面链接中的figure2

image.png

论文中的作图数据是没有提供的，这里我就随便构造一个数据，能够把论文中提供的代码运行通就可以

示例数据集

image.png

读取数据集

library(readxl) dat<-read_excel("data/20230301/20230301.xlsx") dat

作图代码

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) }