帶有嵌套因素的 data.frame 到 igraph 氣泡圖中

Question

我有一個帶有一些分類列和一個數字列的標准 data.Frame。 它代表一個嵌套的實驗設計（但它並不重要），像這樣：

set.seed(1234)
data = data.frame(toplevel=c("A","A","A","A", "B", "B", "B"), 
                  second = c("A1", "A1", "A2", "A2", "B1", "B1", "B2"),
                  experiments = paste0("exp_00", 1:7),
                  values = runif(7, 1,100))
####   toplevel second experiments   values
#### 1        A     A1     exp_001 12.25664
#### 2        A     A1     exp_002 62.60764
#### 3        A     A2     exp_003 61.31820
#### 4        A     A2     exp_004 62.71456
#### 5        B     B1     exp_005 86.23062
#### ...

我想用這個（左邊的情節！）的代碼做同樣的情節： https : //www.r-graph-gallery.com/314-custom-circle-packing-with-several-levels/

我不知道如何將我的數據框變成“igraph”data.Frame 並繼續執行建議繪制的代碼（我沒有from和to列..）。 給定我的示例數據（圓圈大小代表values列），我想要的輸出看起來像右邊的圖。 我嘗試使用graph_from_data_frame失敗

感謝編輯：到目前為止我嘗試的代碼（我只有部分圖表..？）

library(tidyverse); library(igraph); library(ggraph)
edges = rbind.data.frame(data[,1:2] %>% setNames(c("from", "to")), data[, 2:3] %>% setNames(c("from", "to")))
vertices = bind_rows(
  data %>% group_by(toplevel) %>% summarize(values=sum(values)) %>% select(name=toplevel, values),
  data %>% group_by(second) %>% summarize(values=sum(values)) %>% select(name=second, values),
  data %>% select(name=experiments, values)
)
mygraph=graph_from_data_frame(edges, directed = TRUE, vertices = vertices)
ggraph(mygraph, layout = 'circlepack',weight="values") + 
  geom_node_circle() +
  theme_void()

Answer 1

我認為你目前的嘗試絕對是在正確的軌道上。 一個可能有幫助的技巧是添加一個額外的“根”節點，您的兩個頂級節點都連接到該節點。 目前，因為您的頂級節點之間根本沒有連接，所以 ggraph 只繪制其中的一組：

edges = rbind.data.frame(
    data[,1:2] %>% setNames(c("from", "to")), 
    data[, 2:3] %>% setNames(c("from", "to")),
    data.frame(from = c("root", "root"), to = c("A", "B")))
vertices = bind_rows(
    data.frame(name = "root", values = sum(data$values)),
    data %>% group_by(toplevel) %>% summarize(values=sum(values)) %>% select(name=toplevel, values),
    data %>% group_by(second) %>% summarize(values=sum(values)) %>% select(name=second, values),
    data %>% select(name=experiments, values),
)
mygraph=graph_from_data_frame(edges, directed = TRUE, vertices = vertices)
ggraph(mygraph, layout = 'circlepack',weight="values") + 
    geom_node_circle(aes(fill = depth)) +
    geom_node_label(aes(label = name)) +
    theme_void()