使用 R 和 ggplot2 创建基于因子的树状图

Question

这与其说是一种编码，不如说是求助的一般方法 ;-) 我准备了一个 table，其中包含有关生物体的分类信息。但是我想使用这些生物体的 "names"，所以没有任何值或任何可以用来计算距离或聚类的东西（这也是我拥有的所有信息）。我只想使用这些因素来创建一个显示关系的图。我的数据如下所示：

    test2<-structure(list(genus = structure(c(4L, 2L, 7L, 8L, 6L, 1L, 3L, 
5L, 5L), .Label = c("Aminobacter", "Bradyrhizobium", "Hoeflea", 
"Hyphomonas", "Mesorhizobium", "Methylosinus", "Ochrobactrum", 
"uncultured"), class = "factor"), family = structure(c(4L, 1L, 
2L, 3L, 5L, 6L, 6L, 6L, 6L), .Label = c("Bradyrhizobiaceae", 
"Brucellaceae", "Hyphomicrobiaceae", "Hyphomonadaceae", "Methylocystaceae", 
"Phyllobacteriaceae"), class = "factor"), order = structure(c(1L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Caulobacterales", 
"Rhizobiales"), class = "factor"), class = structure(c(1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Alphaproteobacteria", class = "factor"), 
    phylum = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Proteobacteria", class = "factor")), .Names = c("genus", 
"family", "order", "class", "phylum"), class = "data.frame", row.names = c(NA, 
9L))

是否需要人为设置数值来描述层级之间的距离？

Answer 1

这是使用 data.tree 库的尝试

首先在表单中创建一个字符串变量： Proteobacteria/Alphaproteobacteria/Caulobacterales/Hyphomonadaceae/Hyphomonas

library(data.tree)
test2$pathString <- with(test2, 
                               paste(phylum,
                                     class,
                                     order,
                                     family,
                                     genus, sep = "/"))

tree_test2 = as.Node(test2)
plot(tree_test2)

点赞后可以做很多事情：

互动网络：

library(networkD3)
test2_Network <- ToDataFrameNetwork(tree_test2, "name")
simpleNetwork(test2_Network)

或图形样式

library(igraph)
plot(as.igraph(tree_test2, directed = TRUE, direction = "climb"))

查看 vignette

使用 ggplot2:

library(ggraph)
graph = as.igraph(tree_test2, directed = TRUE, direction = "climb")

ggraph(graph, layout = 'kk') + 
  geom_node_text(aes(label = name))+
  geom_edge_link(arrow = arrow(type = "closed", ends = "first",
                               length = unit(0.20, "inches"),
                               angle = 15)) +
  geom_node_point() +
  theme_graph()+
  coord_cartesian(xlim = c(-3,3), expand = TRUE)

或者也许：

ggraph(graph, layout = 'kk') + 
  geom_node_text(aes(label = name),   repel = T)+
  geom_edge_link(angle_calc = 'along',
                 end_cap = circle(3, 'mm'))+ 
  geom_node_point(size = 5) +
  theme_graph()+
  coord_cartesian(xlim = c(-3,3), expand = TRUE)

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