R：绘图太大而无法放入窗口

Question

我用 igraph 包制作了系统发育树图。 问题是，我的树太大而无法放入保存的图像中。 我正在使用 Rstudio，通常手动保存我的绘图。 使用较小的树，我能够放大 Rstudio 的绘图窗口，使绘图适合图像，而节点不会相互重叠。 不幸的是，这不适用于我的最新情节。 我试图用png() 、 pdf()和jpeg()以不同的width和height保存它，但它仍然不适合。 节点彼此重叠或在图像中仅显示部分绘图。 到目前为止，我发现的唯一解决方案是减小标签大小。 但最终，你什么也读不出来。

预先感谢您的帮助。

这是我的代码：

id <- c("Spirochaetota","Brachyspirae","Brevinematia","Leptospirae","Spirochaetia","sk6","Brachyspirales","Brachyspiraceae","Brachyspira",
      "Brevinematales","bo1","Brevinemataceae","Brevinema","bf2","Leptospirales","Leptonemataceae","Leptonema","lg2","Leptospiraceae","Leptospira",
      "LeptospiraA","LeptospiraB","lg3","lf1","Turneriellales","Turneriellaceae","Turneriella","tf1","Borreliales","Borreliaceae","Borrelia",
      "Borreliella","Sphaerochaetales","Sphaerrochaetaceae","Sphaerochaeta","SphaerochaetaA","sg15","SpirochaetalesA","SpirochaetaceaeA",
      "SpirochaetaA","sf1","SpirochaetalesC","Alkalispirochaetaceae","Alkalispirochaeta","Salinispiraceae","Salinispira","SpirochaetaD","sg1",
      "sf6","SpirochaetalesD","sdf1","SpirochaetalesE","SpirochaetaceaeB","Oceanispirochaeta","SpirochaetaE","SpirochaetaF","SpirochaetaG","sg2",
      "Treponematales","Treponemataceae","Treponema","TreponemaB","TreponemaC","TreponemaD","TreponemaF","tg7","TreponemataceaeB","TreponemaE",
      "TreponemaG","TreponemaH","tg5","tf3","so11")

links <- data.frame(from = c("Spirochaetota","Spirochaetota","Spirochaetota","Spirochaetota","Spirochaetota","Brachyspirae",
                "Brachyspirales","Brachyspiraceae","Brevinematia","Brevinematia","Brevinematales","Brevinemataceae",
                "Brevinematales","Leptospirae","Leptospirales","Leptonemataceae","Leptonemataceae","Leptospirales",
                "Leptospiraceae","Leptospiraceae","Leptospiraceae","Leptospiraceae","Leptospirales","Leptospirae",
                "Turneriellales","Turneriellaceae","Turneriellales","Spirochaetia","Borreliales","Borreliaceae",
                "Borreliaceae","Spirochaetia","Sphaerochaetales","Sphaerrochaetaceae","Sphaerrochaetaceae","Sphaerrochaetaceae",
                "Spirochaetia","SpirochaetalesA","SpirochaetaceaeA","SpirochaetalesA","Spirochaetia","SpirochaetalesC",
                "Alkalispirochaetaceae","SpirochaetalesC","Salinispiraceae","Salinispiraceae","Salinispiraceae","SpirochaetalesC",
                "Spirochaetia","SpirochaetalesD","Spirochaetia","SpirochaetalesE","SpirochaetaceaeB","SpirochaetaceaeB",
                "SpirochaetaceaeB","SpirochaetaceaeB","SpirochaetaceaeB","Spirochaetia","Treponematales","Treponemataceae",
                "Treponemataceae","Treponemataceae","Treponemataceae","Treponemataceae","Treponemataceae","Treponematales",
                "TreponemataceaeB","TreponemataceaeB","TreponemataceaeB","TreponemataceaeB","Treponematales","Spirochaetia"),
                to = c("Brachyspirae","Brevinematia","Leptospirae","Spirochaetia","sk6","Brachyspirales",
                       "Brachyspiraceae","Brachyspira","Brevinematales","bo1","Brevinemataceae","Brevinema",
                       "bf2","Leptospirales","Leptonemataceae","Leptonema","lg2","Leptospiraceae",
                       "Leptospira","LeptospiraA","LeptospiraB","lg3","lf1","Turneriellales",
                       "Turneriellaceae","Turneriella","tf1","Borreliales","Borreliaceae","Borrelia",
                       "Borreliella","Sphaerochaetales","Sphaerrochaetaceae","Sphaerochaeta","SphaerochaetaA","sg15",
                       "SpirochaetalesA","SpirochaetaceaeA","SpirochaetaA","sf1","SpirochaetalesC","Alkalispirochaetaceae",
                       "Alkalispirochaeta","Salinispiraceae","Salinispira","SpirochaetaD","sg1","sf6",
                       "SpirochaetalesD","sdf1","SpirochaetalesE","SpirochaetaceaeB","Oceanispirochaeta","SpirochaetaE",
                       "SpirochaetaF","SpirochaetaG","sg2","Treponematales","Treponemataceae","Treponema",
                       "TreponemaB","TreponemaC","TreponemaD","TreponemaF","tg7","TreponemataceaeB",
                       "TreponemaE","TreponemaG","TreponemaH","tg5","tf3","so11"))

net <- graph_from_data_frame(d = links, vertices = id, directed = T)

lay = layout.reingold.tilford(net)

plot(net, vertex.shape = "none", 
     vertex.label.font = 3,
     vertex.label.cex = 0.3,
     edge.arrow.size = 0.3,
     rescale = F,
     ylim = c(0.7,3.4),xlim = c(-8,23.2), asp = 0,
     layout = lay)

如果一切正常，它应该看起来类似于这棵较小的树。 这个不包括上面代码的节点：

这是我到目前为止的大树的结果。 它包含上面代码中的节点：

到目前为止，我想出的唯一解决方案是以某种方式将绘图放入绘图面板并将其另存为 SVG 文件。 之后，我使用inkscape对其进行了编辑：

Answer 1

您可以将树形图绘制为树状图。 从左到右绘制它允许将所有分类单元标签放在一个可读列中：

library(igraph)
net <- graph_from_data_frame(d = links, vertices = id, directed = F)
lay <- layout.reingold.tilford(net)

plot_dendrogram(cluster_fast_greedy(net))

还有：

links %>%
  graph_from_data_frame() %>%
  as_adjacency_matrix() %>%
  dist() %>%
  hclust() %>%
  as.dendrogram() %>%
  plot()