我尝试遵循Guy的R代码创建圆形迁移图。我的文件与他通过“migest”软件包提供的文件类似(science / regions_custom)。我的数据文件示例是“regions_oceanos”:
- - - 1 2 4 3
- - - Pacífico Índico Mediterráneo Atlántico
1 160,0,125 Pacífico 245.025 1.70210026 0.09857195 1.7337982
2 0,255,233 Índico 0.4165425 242.575 3.9052666 6.9741618
4 125,175,0 Mediterráneo 3.05222742 5.99567776 11.125 5.7953056
3 255,219,0 Atlántico 2.63735109 7.51662301 4.3093533 36.625
R代码是:
library("migest")
m<-read.table("region_reciente.txt", skip=2, stringsAsFactors=FALSE)
df1<-m[,1:3]
names(df1)<-c("order","rgb","region")
df1$region<-gsub("_", " ", df1$region)
m<-m[,-(1:3)]/1e06
m<-as.matrix(m)
dimnames(m)<-list(orig=df1$region,dest=df1$region)
library("plyr")
df1<-arrange(df1, order)
df1$region <- factor(df1$region, levels=df1$region)
m<-m[levels(df1$region),levels(df1$region)]
df1$xmin <- 0
df1$xmax <- rowSums(m)+colSums(m)
n<-nrow(df1)
df1 <- cbind(df1, matrix(as.numeric(unlist(strsplit(df1$rgb,","))),nrow=n, byrow=TRUE) )
names(df1)[ncol(df1)-2:0]<-c("r","g","b")
df1$rcol<-rgb(df1$r, df1$g, df1$b, max = 255)
df1$lcol<-rgb(df1$r, df1$g, df1$b, alpha=200, max = 255)
library("circlize")
par(mar=rep(0,4))
circos.clear()
circos.par(cell.padding=c(0,0,0,0), track.margin=c(0,0.1), start.degree = 90, gap.degree =4)
circos.initialize(factors = df1$region, xlim = cbind(df1$xmin, df1$xmax))
circos.trackPlotRegion(ylim = c(0, 1), factors = df1$region, track.height=0.1, bg.border = NA, bg.col = NA, bg.lty =0, bg.lwd=0.0001,
panel.fun = function(x, y) {
name = get.cell.meta.data("sector.index")
i = get.cell.meta.data("sector.numeric.index")
xlim = get.cell.meta.data("xlim")
ylim = get.cell.meta.data("ylim")
circos.text(x=mean(xlim), y=2.2, labels=name, facing = "bending", cex=0.8)
circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2], ytop=ylim[2],
col = df1$rcol[i], border=df1$rcol[i])
circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2]-rowSums(m)[i], ytop=ylim[1]+0.3,
col = "white", border = "white")
circos.rect(xleft=xlim[1], ybottom=0.3, xright=xlim[2], ytop=0.32, col = "white", border = "white")
circos.axis(labels.cex=0.8, direction = "outside", major.at=seq(0,floor(df1$xmax)[i]), minor.ticks=1,
labels.away.percentage = 0.15)
})
df1$sum1 <- colSums(m)
df1$sum2 <- numeric(n)
df2<-cbind(as.data.frame(m),orig=rownames(m), stringsAsFactors=FALSE)
df2<-reshape(df2, idvar="orig", varying=list(1:n), direction="long", timevar="dest", time=rownames(m), v.names = "m")
df2<-arrange(df2,desc(m))
df2<-subset(df2, m>quantile(m,0.65))
for(k in 1:nrow(df2)){
i<-match(df2$orig[k],df1$region)
j<-match(df2$dest[k],df1$region)
circos.link(sector.index1=df1$region[i], point1=c(df1$sum1[i], df1$sum1[i] + abs(m[i, j])),
sector.index2=df1$region[j], point2=c(df1$sum2[j], df1$sum2[j] + abs(m[i, j])),
col = df1$lcol[i])
df1$sum1[i] = df1$sum1[i] + abs(m[i, j])
df1$sum2[j] = df1$sum2[j] + abs(m[i, j])
}
而且，如您所见，我获得了这个very cool graph，但是其中的链接不一定代表我的矩阵。例如，您可以看到从太平洋流域到地中海流域和地中海流域，或者从大西洋流域到地中海流域都没有流量，但是在矩阵中，我给出了那些与实际绘制的那些相似的值。可能与“注意”有关，该代码在创建绘图区域后出现:(注意:1点位于扇区“Pacífico”的磁迹区域中，轨迹为“1”)。但是我不确定如何处理。我将非常感谢任何反馈和意见
最佳答案
线
df2 <- subset(df2, m>quantile(m,0.65))
确保仅绘制最大流量。鉴于您只有四个区域，因此您可能不需要此功能，听起来好像您想查看所有流程。
另外，我还没有更新migest包中的演示脚本的CRAN版本。使用github上的版本可能会更好，
https://github.com/gjabel/migest/tree/master/demo或...现在，使用
chordDiagram函数可以更加轻松地绘制这些图:library("circlize")
m <- read.table("region_reciente.txt", skip=2, stringsAsFactors=FALSE)
#data.frame for details on each region
df1 <- m[,1:3]
names(df1) <- c("order","rgb","region")
n <- nrow(df1)
df1 <- cbind(df1, matrix(as.numeric(unlist(strsplit(df1$rgb,","))),nrow=n, byrow=TRUE) )
names(df1)[ncol(df1)-2:0] <- c("r","g","b")
df1$rcol <- rgb(df1$r, df1$g, df1$b, max = 255)
#flow matrix
m <- m[,-(1:3)]
m <- as.matrix(m)
dimnames(m) <- list(orig=df1$region, dest=df1$region)
chordDiagram(m, directional = TRUE, grid.col=df1$rcol)
关于r - 循环迁移图缺少的链接，我们在Stack Overflow上找到一个类似的问题：https://stackoverflow.com/questions/28891125/