ggalluvial：第一轴和第二轴的相同地层顺序

Question

我想保持冲积地块的第二个轴与第一个轴的顺序相同。也就是说，由于第一个轴是第二个轴的更高级别的分类法，其主要目的是显示生物体的概览和分组，以增强图表的可读性。为此，我尝试手动订购地层。然而，我所做的只是重新洗牌矿脉而不是地层（例如从这个 tutorial 或玩 lode.guidance）。

有人知道如何解决这个问题吗？最后，第一轴和第二轴之间的所有矿脉应该水平流动，然后从第二轴到第三轴按原样排序。

数据的简短版本（仍然很广泛，抱歉）：

taxa <- structure(list(Order = structure(c(6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
                                           6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
                                           6L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L,
                                           9L, 9L, 19L, 19L, 19L, 19L, 19L, 19L,
                                           19L, 19L, 19L, 19L, 19L, 19L, 19L,
                                           19L, 27L, 27L, 27L, 27L, 27L, 27L,
                                           27L, 27L, 27L, 27L, 27L, 27L, 27L,
                                           32L, 32L, 32L, 32L, 32L, 32L, 32L,
                                           32L, 32L, 32L, 32L, 32L, 32L),
                                         .Label = c("Adinetida", "Cercomonadidae_or",
                                                    "Cercozoa_unclassified",
                                                    "Chaetopeltidales",
                                                    "Chlorophyta_ph_unclassified",
                                                    "Chromulinales",
                                                    "Chrysophyceae_unclassified",
                                                    "Chytridiomycetes_unclassified",
                                                    "Conthreep", "Craspedida_or",
                                                    "Cryomonadida", "Cryptomonadales",
                                                    "Cystobasidiales",
                                                    "Cystobasidiomycetes_unclassified",
                                                    "Cystofilobasidiales",
                                                    "Dinophyceae_unclassified",
                                                    "Diplogasterida",
                                                    "Glissomonadida_or",
                                                    "Helotiales", "Imbricatea_unclassified",
                                                    "Incertae_Sedis",
                                                    "Intramacronucleata_unclassified",
                                                    "Leotiomycetes_unclassified", "LG08-10_or",
                                                    "Litostomatea", "Monhysterida",
                                                    "Ochromonadales",
                                                    "Ochrophyta_ph_unclassified",
                                                    "Parachela",
                                                    "Peronosporomycetes_or",
                                                    "Phragmoplastophyta_unclassified",
                                                    "Saccharomycetales",
                                                    "Spirotrichea", "Spongomonadida",
                                                    "Thecofilosea_unclassified",
                                                    "Tremellales", "Tremellomycetes_or",
                                                    "Tremellomycetes_unclassified",
                                                    "Trichosporonales"),
                                         class = "factor"),
              Genus = c(paste(rep("Poterioochromonas", 19)),
                        paste(rep("Colpoda", 9)),
                        paste(rep("Colpodea_unclassified", 24)),
                        paste(rep("Colpodida_ge", 28)),
                        paste(rep("Conthreep_unclassified", 4)),
                        "Cryptocaryon", "Cyclidium",
                        paste(rep("Nassophorea_unclassified", 2)),
                        "Platyophrya", paste(rep("Tetrahymena", 5)),
                        paste(rep("uncultured", 3)),
                        paste(rep("uncultured_ge", 4)), "Glarea",
                        paste(rep("Helotiales_unclassified_ge", 13)),
                        paste(rep("Chrysolepidomonas", 12)), "Ochromonas",
                        paste(rep("Debaryomycetaceae_unclassified", 3)),
                        "Pichiaceae_unclassified_ge",
                        paste(rep("Saccharomycetaceae_unclassified", 5)),
                        paste(rep("Yarrowia", 4))),
              Freq = rep(1, 141),
              Habitat = c("B", "B", "B", "B", "B", "B", "B","B", "B", "B", "B",
                          "B", "B", "B", "B", "B", "B", "B", "B", "A", "A", "A",
                          "B", "A", "A", "B", "B", "B", "B", "A", "A", "A", "A",
                          "B", "A", "A", "A", "A", "B", "A", "B", "B", "A", "B",
                          "B", "B", "A", "A", "A", "B", "B", "B", "A", "A", "A",
                          "A", "A", "A", "A", "A", "B", "A", "B", "A", "B", "B",
                          "A", "A", "B", "B", "A", "B", "A", "B", "B", "A", "A",
                          "B", "B", "B", "B", "B", "B", "B", "B", "B", "A", "A",
                          "B", "A", "A", "B", "B", "B", "A", "B", "B", "A", "B",
                          "B", "B", "A", "A", "A", "A", "A", "A", "A", "A", "B",
                          "A", "B", "A", "B", "A", "A", "A", "B", "B", "B", "B",
                          "B", "B", "B", "B", "B", "B", "B", "B", "B", "B", "B",
                          "A", "A", "B", "A", "B", "A", "B", "B", "B")),
              class = "data.frame", row.names = seq(1:141))

这里是三个轴按字母顺序排列的冲积图：

library("ggalluvial")

ggplot(data = taxa,
       aes(axis1 = Order, axis2 = Genus, axis3 = Habitat, y = Freq)) +
  stat_alluvium(aes(fill = Habitat)) +
  geom_stratum(linetype = 1, lwd = 0.01) +
  geom_text(stat = "stratum", infer.label = TRUE, size = 3) +
  theme_void() +
  theme(legend.position = "none")

Answer 1

正如@s_t 所建议的，这应该可以通过使 taxa$Genus 成为因子变量而不是字符变量来解决。但是 as.factor() 将因子水平按字母顺序排列，这不是您想要的。通过按照它们在 taxa 中出现的顺序指定级别，以下代码在第二个轴中重新排序层，同时保持其他轴不变。结果情节是你想要的吗？（省略了从您的问题复制的代码。）

# ensure that 'Genus' is a factor with levels in order of appearance
taxa$Genus <- factor(taxa$Genus, levels = as.character(unique(taxa$Genus)))
# plot
ggplot(data = taxa,
       aes(axis1 = Order, axis2 = Genus, axis3 = Habitat, y = Freq)) +
  stat_alluvium(aes(fill = Habitat)) +
  geom_stratum(linetype = 1, lwd = 0.01) +
  geom_text(stat = "stratum", infer.label = TRUE, size = 3) +
  theme_void() +
  theme(legend.position = "none")

^{由 reprex package (v0.3.0)}

于 2020-05-16 创建

ggalluvial：第一轴和第二轴的相同地层顺序

ggalluvial: identical strata order of the first and second axis

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