Question

我尝试使用r库＆＃34; circlize＆＃34;复制此网站https://gjabel.wordpress.com/2014/03/28/circular-migration-flow-plots-in-r/的图表。不幸的是我有两个问题：

首先，我收到了所有绘图区域的警告（即Note: 1 point is out of plotting region in sector 'Mexico', track '1'）。我认为问题出在circos.text和circos.axis，因为我将它们与direction一起使用，这是一个已弃用的函数。但是，使用facing代替direction，问题仍然存在。所以我想我并不理解这个警告的含义。你有一些提示可以帮助我吗？

此外，在我的情节中，链接距离细分非常远。因此，我试图减少track.margin，它解决了这个问题，但现在这些段的名称都在边缘之外，我无法将它们可视化。有没有更好的方法来解决这个问题？

这是我到目前为止所写的内容（几乎全部来自此网站https://github.com/null2/globalmigration）

library("circlize")
library("plyr")
library("migest")
#load data
m<-read.table(system.file("science", "country_custom.txt", package = "migest"), skip=2, stringsAsFactors=FALSE)
#1)a data.frame to store information on each segment of the circle to be plotted
df1<-m[,1:3]
names(df1)<-c("order","rgb","region")
df1$region<-gsub("\\.", "\n", df1$region)
#2) a matrix containing the flow data (in this example only 28 countries)
m<-m[,-(1:3)]/1e05
m<-as.matrix(m)
dimnames(m)<-list(orig=df1$region,dest=df1$region)
#sort order of data.frame and matrix for plotting in circos    
df1<-arrange(df1, order) #reordering a data frame by its columns
df1$region <- factor(df1$region, levels=df1$region)
m<-m[levels(df1$region),levels(df1$region)]
#define ranges of circos sectors and their colors (both of the sectors and the links)
#determine the length of segments on the outside of the plot.
df1$xmin <- 0
df1$xmax <- rowSums(m)+colSums(m) #inflows+outflows
#set the colour names for segments and flows
n<-nrow(df1)
df1 <- cbind(df1, matrix(as.numeric(unlist(strsplit(df1$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)
##plot sectors
windows()
par(mar=rep(0,4))
circos.clear()
#1)basic circos graphic parameters
circos.par(cell.padding=c(0,0,0,0), track.margin=c(0,0.01), start.degree = 90, gap.degree =4)
#2)sector details
circos.initialize(factors = df1$region, xlim = cbind(df1$xmin, df1$xmax))
#3)plot sectors
circos.trackPlotRegion(ylim = c(0, 1), factors = df1$region, track.height=0.1,
       panel.fun = function(x, y) {
         #select details of current sector
         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")

         #text direction (dd) and adjusmtents (aa)
         theta = circlize(mean(xlim), 1.3)[1, 1] %% 360
         dd <- ifelse(theta < 90 || theta > 270, "vertical_right", "vertical_left")
         aa = c(1, 0.5)
         if(theta < 90 || theta > 270)  aa =c(0, 0.5)

         #plot country labels
         circos.text(x=mean(xlim), y=1.7, labels=name, direction = dd,
         cex=0.6,adj = aa)
         #circos.text(x=mean(xlim), y=2, labels=name, facing = "bending",cex=0.6)             

         #plot main sector
         circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2], ytop=ylim[2], 
         col = df1$rcol[i], border=df1$rcol[i])

         #blank in part of main sector
         circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2]-rowSums(m)[i], ytop=ylim[1]+0.3, 
         col = "white", border = "white")

         #white line all the way around
         circos.rect(xleft=xlim[1], ybottom=0.3, xright=xlim[2], ytop=0.32, col = "white", border = "white")

         #plot axis
         #NOTE: Ticks indicate the number of migrants in 100s.
         circos.axis(labels.cex=0.6, direction = "outside", major.at=seq(from=0,to=floor(df1$xmax)[i],by=5), 
         minor.ticks=1, labels.away.percentage = 0.15)
       })

非常感谢你的帮助。

编辑：我添加了脚本的第二部分，因为似乎有必要解决第二个问题。

#plot links
#create a new dataframe containing the long form of the matrix m
#add sum values to df1, marking the x-position of the first links out (sum1) and in (sum2). Updated for further links in loop below.
df1$sum1 <- colSums(m) #outflows
df1$sum2 <- numeric(n)
#create a data.frame of the flow matrix sorted by flow size, to allow largest flow plotted first
df2<-cbind(as.data.frame(m),orig=rownames(m),  stringsAsFactors=FALSE)
#long matrix
df2<-reshape(df2, idvar="orig", varying=list(1:n), direction="long", timevar="dest", time=rownames(m),  v.names = "m") 
df2<-arrange(df2,desc(m))
#keep only the largest flows to avoid clutter
df2<-subset(df2, m>quantile(m,0.925))
#plot links
for(k in 1:nrow(df2)){
require("circlize")
#i,j reference of flow matrix
#note: you are selecting the states in region1 according to the edgelist in region2
i<-match(df2$orig[k],df1$region)
j<-match(df2$dest[k],df1$region)
#plot link
#sector.index1=sender
#point1=size of the base of the link at the origin
#We set the origin segment to start at the current sum of outflows from the sender country (df1$sum1[i])    
#We set the end of the segment outflow equal to the total outflows from the sender country, plus the flow from the edge we considered
circos.link(sector.index1=df1$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]) #, top.ratio==0.66, top.ratio.low==0.67)
#note: The height and thickness of the link at its mid-point is determined by the top.ratio and the top.ratio.low argument
#update sum1 and sum2 for use when plotting the next link
df1$sum1[i] = df1$sum1[i] + abs(m[i, j])
df1$sum2[j] = df1$sum2[j] + abs(m[i, j])
}

Answer 1

您可以在当前版本的 circlize 中查看chordDiagram()。 chordDiagram()是一个灵活的函数，它可以制作这样的和弦图（即带有链接的圆形图）。此功能是在 circlize 的最新版本中引入的，您不需要太多代码来自定义Chord Diagram。该软件包附带了一个小插图，为您提供如何制作简单或复杂的和弦图的详细介绍。

快速演示再现您感兴趣的人物如下：

mat = matrix(runif(36), 6)
rownames(mat) = letters[1:6]
colnames(mat) = letters[1:6]

library(circlize)
circos.par(gap.degree = 8)
chordDiagram(mat, grid.col = 1:6, directional = TRUE, annotationTrack = "grid",
  preAllocateTracks = list(list(track.height = 0.05),
                           list(track.height = 0.05)))
circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.index = get.cell.meta.data("sector.index")
  circos.text(mean(xlim), mean(ylim), sector.index, facing = "inside", niceFacing = TRUE)
}, bg.border = NA)
circos.trackPlotRegion(track.index = 2, panel.fun = function(x, y) {
  circos.axis("bottom", major.tick.percentage = 0.2, labels.cex = 0.4)
}, bg.border = NA)
circos.clear()

enter image description here

Answer 2

关于笔记消息的第一个问题并不是真正的问题。无论警告如何，您仍然可以获得所需的情节。您可以使用

来制作消息

circos.par(points.overflow.warning=FALSE)

第二个问题是最近更新circlize包的结果。您需要通过添加

来更改其初始设置中的曲目边距

circos.par(track.margin=c(0,0))

在circos.trackPlotRegion命令后以及通过circos.link循环中的for函数绘制链接之前。

抱歉这些问题。我一直想在migest软件包中更新演示文件一段时间，但在假日期间有点忘了它。

Answer 3

正如作者解释here

“points.overflow.warning”因为每个单元格实际上都不是真实的绘图区域但只有一个普通的矩形，它不会消除从该区域绘制的点。所以，如果有一些要点在绘图区域中，circlize将继续绘制点和打印警告。在某些情况下，从中抽出一些东西绘图区域很有用，例如绘制一些图例或文本。设置这个值为FALSE以关闭警告。

由canvas.xlim和canvas.ylim（在上面的同一页中描述），您可以设置画布以避免或忽略警告。

R circlize - 绘制边距和绘制区域

3 个答案: