r - R中的网络和弦图出现问题

我有一些类似于data.frame d的数据，如下所示。

d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243",
                           "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007",
                           "GP3398", "GP6720", "KP808", "KP1154", "KP748", "GP4263", "GP1132",
                           "GP5881", "GP6291", "KP1004", "KP1998", "GP4123", "GP5930", "KP1070",
                           "KP905", "KP579", "KP1100", "KP587", "GP913", "GP4864", "KP1513",
                           "GP5979", "KP730", "KP1412", "KP615", "KP1315", "KP993", "GP1521",
                           "KP1034", "KP651", "GP2876", "GP4715", "GP5056", "GP555", "GP408",
                           "GP4217", "GP641"),
                    Type = c("B", "A", "B", "A", "B", "B", "B",
                             "B", "B", "A", "A", "A", "A", "B", "B", "B", "A", "A", "A", "A",
                             "B", "B", "A", "A", "B", "B", "B", "B", "B", "A", "A", "B", "A",
                             "B", "B", "B", "B", "B", "A", "B", "B", "A", "A", "A", "A", "A",
                             "A", "A"),
                    Set = c(15L, 1L, 10L, 21L, 5L, 9L, 12L, 15L, 16L,
                            19L, 22L, 3L, 12L, 22L, 15L, 25L, 10L, 25L, 12L, 3L, 10L, 8L,
                            8L, 20L, 20L, 19L, 25L, 15L, 6L, 21L, 9L, 5L, 24L, 9L, 20L, 5L,
                            2L, 2L, 11L, 9L, 16L, 10L, 21L, 4L, 1L, 8L, 5L, 11L), Loc = c(3L,
                                                                                          2L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 2L, 1L, 3L,
                                                                                          2L, 2L, 2L, 3L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 3L, 1L, 3L, 3L,
                                                                                          1L, 3L, 2L, 3L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 2L, 3L, 3L)),
               .Names = c("ID", "Type", "Set", "Loc"), class = "data.frame",
               row.names = c(NA, -48L))

我想使用类似于下图的和弦图来探索d$ID成员之间的关系。

似乎在R中有几个选项可以这样做。 (Chord diagram in R)。

在我的数据中，关系是根据d$Set(不是定向的)，而分组是根据d$Loc。以下是我将塞瑟尔关系映射为和弦图的尝试。

尝试1:使用igraph
我已经尝试过igraph，根据节点的大小如下。

# Get vertex relationships
sets <- unique(d$Set[duplicated(d$Set)])
rel <-  vector("list", length(sets))
for (i in 1:length(sets)) {
  rel[[i]] <- as.data.frame(t(combn(subset(d, d$Set ==sets[i])$ID, 2)))
}
library(data.table)
rel <- rbindlist(rel)

# Get the graph
g <- graph.data.frame(rel, directed=F, vertices=d)
clr <- as.factor(V(g)$Loc)
levels(clr) <- c("salmon", "wheat", "lightskyblue")
V(g)$color <- as.character(clr)

# Plot
plot(g, layout = layout.circle, vertex.size=degree(g)*5, vertex.label=NA)

如何将绘图修改为第一个图形？似乎没有修改igraph layout.circle的选项。

尝试2:使用Circlize
在R包circlize中，看起来更平滑的贝塞尔曲线和分组是可能的。但是在这里，我无法将节点分组，也无法根据程度调整其大小，因为它们被绘制为扇区。

par(mar = c(1, 1, 1, 1), lwd = 0.1, cex = 0.7)
circos.initialize(factors = as.factor(d$ID), xlim = c(0, 10))
circos.trackPlotRegion(factors = as.factor(d$ID), ylim = c(0, 0.5), bg.col = V(g)$color,
                       bg.border = NA, track.height = 0.05)
for(i in 1:nrow(rel)) {
  circos.link(rel[i,1], 0, rel[i,2],0, h = 0.4)

}

但是，这里没有修改节点的选项。实际上它们只能绘制为扇区吗？在这种情况下，是否可以根据程度将扇区修改为大小呈圆形的节点？

尝试3:使用edgebundleR(https://github.com/garthtarr/edgebundleR)

require(edgebundleR)
edgebundle(g,tension = 0.1,cutoff = 0.5, fontsize = 18,padding=40)

在这里看来，修改美学的选择有限。

最佳答案

我对edgebundleR做了很多更改。这些现在在主仓库中。以下代码将使您接近所需的结果。 live example

# devtools::install_github("garthtarr/edgebundleR")

library(edgebundleR)
library(igraph)
library(data.table)

d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243",
                           "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007",
                           "GP3398", "GP6720", "KP808", "KP1154", "KP748", "GP4263", "GP1132",
                           "GP5881", "GP6291", "KP1004", "KP1998", "GP4123", "GP5930", "KP1070",
                           "KP905", "KP579", "KP1100", "KP587", "GP913", "GP4864", "KP1513",
                           "GP5979", "KP730", "KP1412", "KP615", "KP1315", "KP993", "GP1521",
                           "KP1034", "KP651", "GP2876", "GP4715", "GP5056", "GP555", "GP408",
                           "GP4217", "GP641"),
                    Type = c("B", "A", "B", "A", "B", "B", "B",
                             "B", "B", "A", "A", "A", "A", "B", "B", "B", "A", "A", "A", "A",
                             "B", "B", "A", "A", "B", "B", "B", "B", "B", "A", "A", "B", "A",
                             "B", "B", "B", "B", "B", "A", "B", "B", "A", "A", "A", "A", "A",
                             "A", "A"),
                    Set = c(15L, 1L, 10L, 21L, 5L, 9L, 12L, 15L, 16L,
                            19L, 22L, 3L, 12L, 22L, 15L, 25L, 10L, 25L, 12L, 3L, 10L, 8L,
                            8L, 20L, 20L, 19L, 25L, 15L, 6L, 21L, 9L, 5L, 24L, 9L, 20L, 5L,
                            2L, 2L, 11L, 9L, 16L, 10L, 21L, 4L, 1L, 8L, 5L, 11L), Loc = c(3L,
                                                                                          2L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 2L, 1L, 3L,
                                                                                          2L, 2L, 2L, 3L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 3L, 1L, 3L, 3L,
                                                                                          1L, 3L, 2L, 3L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 2L, 3L, 3L)),
               .Names = c("ID", "Type", "Set", "Loc"), class = "data.frame",
               row.names = c(NA, -48L))

# let's add Loc to our ID
d$key <- d$ID
d$ID <- paste0(d$Loc,".",d$ID)

# Get vertex relationships
sets <- unique(d$Set[duplicated(d$Set)])
rel <-  vector("list", length(sets))
for (i in 1:length(sets)) {
  rel[[i]] <- as.data.frame(t(combn(subset(d, d$Set ==sets[i])$ID, 2)))
}

rel <- rbindlist(rel)

# Get the graph
g <- graph.data.frame(rel, directed=F, vertices=d)
clr <- as.factor(V(g)$Loc)
levels(clr) <- c("salmon", "wheat", "lightskyblue")
V(g)$color <- as.character(clr)
V(g)$size = degree(g)*5
# Plot
plot(g, layout = layout.circle, vertex.label=NA)


edgebundle( g )->eb

eb

关于r - R中的网络和弦图出现问题，我们在Stack Overflow上找到一个类似的问题：https://stackoverflow.com/questions/30708674/