R circlize - 绘图边距和绘图区域
R circlize - plot margins and plotting regions
我正在尝试使用 r 库 "circlize" 复制本网站 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 中，因为我将它们与 direction 一起使用，这是一个已弃用的函数。但是同样使用facing代替direction，问题依旧。所以我想我不明白这个警告的意思。你有什么提示可以帮助我吗？
此外，在我的情节中，链接离片段很远。因此，我试图减少 track.margin，这解决了问题，但现在段的名称在边缘之外，我无法将它们可视化。有没有更好的办法解决这个问题？
这是我目前为止写的（几乎全部取自本站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$xmax)[i],by=5),
minor.ticks=1, labels.away.percentage = 0.15)
})
非常感谢您的帮助。
编辑：
我添加了脚本的第二部分，因为似乎有必要解决第二个问题。
#plot links
#create a new dataframe containing the long form of the matrix m
#add sum values to df1, marking the x-position of the first links out (sum1) and in (sum2). Updated for further links in loop below.
df1$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])
}
关于注释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
制服消息
circos.par(points.overflow.warning=FALSE)
第二个问题是 circlize 包最近更新的结果。您需要通过添加
来更改初始设置的轨道边距
circos.par(track.margin=c(0,0))
在 circos.trackPlotRegion 命令之后和通过 for 循环中的 circos.link 函数绘制链接之前。
抱歉出现问题。一段时间以来，我一直想更新 migest 包中的演示文件，但有点忘记了假期。
您可以在 circlize 当前版本中查看 chordDiagram()。 chordDiagram() 是一个灵活的功能，可以制作这样的弦图（即内部有链接的圆形图）。
此功能是在 circlize 的最新版本中引入的，您不需要太多代码即可 self-define 和弦图。包装内还有小插曲，详细介绍如何制作简单或复杂的和弦图。
复制您感兴趣的图形的快速演示如下：
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()
正如作者所解释的那样here
"points.overflow.warning" Since each cell is in fact not a real
plotting region but only an ordinary rectangle, it does not eliminate
points that are plotted out of the region. So if some points are out
of the plotting region, circlize would continue drawing the points
and printing warnings. In some cases, draw something out of the
plotting region is useful, such as draw some legend or text. Set this
value to FALSE to turn off the warnings.
通过 canvas.xlim 和 canvas.ylim（在上面同一页中描述），您可以设置 canvas 以避免或忽略警告。
我正在尝试使用 r 库 "circlize" 复制本网站 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 中，因为我将它们与 direction 一起使用，这是一个已弃用的函数。但是同样使用facing代替direction，问题依旧。所以我想我不明白这个警告的意思。你有什么提示可以帮助我吗？
此外，在我的情节中，链接离片段很远。因此，我试图减少 track.margin，这解决了问题，但现在段的名称在边缘之外，我无法将它们可视化。有没有更好的办法解决这个问题？
这是我目前为止写的（几乎全部取自本站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)
})
非常感谢您的帮助。
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])
}
关于注释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
制服消息circos.par(points.overflow.warning=FALSE)
第二个问题是 circlize 包最近更新的结果。您需要通过添加
来更改初始设置的轨道边距circos.par(track.margin=c(0,0))
在 circos.trackPlotRegion 命令之后和通过 for 循环中的 circos.link 函数绘制链接之前。
抱歉出现问题。一段时间以来，我一直想更新 migest 包中的演示文件，但有点忘记了假期。
您可以在 circlize 当前版本中查看 chordDiagram()。 chordDiagram() 是一个灵活的功能，可以制作这样的弦图（即内部有链接的圆形图）。
此功能是在 circlize 的最新版本中引入的，您不需要太多代码即可 self-define 和弦图。包装内还有小插曲，详细介绍如何制作简单或复杂的和弦图。
复制您感兴趣的图形的快速演示如下：
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()
正如作者所解释的那样here
"points.overflow.warning" Since each cell is in fact not a real plotting region but only an ordinary rectangle, it does not eliminate points that are plotted out of the region. So if some points are out of the plotting region,
circlizewould continue drawing the points and printing warnings. In some cases, draw something out of the plotting region is useful, such as draw some legend or text. Set this value toFALSEto turn off the warnings.
通过 canvas.xlim 和 canvas.ylim（在上面同一页中描述），您可以设置 canvas 以避免或忽略警告。