Невозможно изменить порядок осей в галлювиальном режиме

Одним из вариантов достижения желаемого результата было бы избавиться от общих уровней для обоих factor, для чего я просто добавляю суффикс "_2" к post_transplant_drug. После этого мы можем избавиться от суффикса, используя, например. gsub():

library(ggalluvial)
#> Loading required package: ggplot2

top_transitions$post_transplant_drug <- factor(
  paste0(top_transitions$post_transplant_drug, "_2"),
  levels = paste0(
    c(
      "DPP4 inhibitors", "Insulin + Sulfonylureas",
      "Insulin", "Insulin + DPP4 inhibitors", "None",
      "Insulin + GLP-1 RAs", "Biguanides", "Sulfonylureas"
    ), "_2"
  )
)

names(color_palette) <- paste0(names(color_palette), "_2")

ggplot(top_transitions, aes(
  axis1 = last_pre_tx_drug,
  axis2 = post_transplant_drug, y = N
)) +
  geom_alluvium(aes(fill = post_transplant_drug),
    width = 1 / 25, knot.pos = 0.1, curve_type = "sigmoid"
  ) +
  geom_stratum(width = 1 / 5, fill = "#F0F0F0", color = "#808080") +
  geom_text(
    stat = "stratum", aes(label = after_stat(
      gsub("_2", "", stratum)
    )),
    size = 3.5, color = "#333333",
    family = "Helvetica Neue", fontface = "bold",
    hjust = 0.5, vjust = 0.5
  ) +
  scale_x_discrete(
    limits = c("last_pre_tx_drug", "post_transplant_drug"),
    labels = c(
      "Last Regimen Used\nPre-Transplant",
      "First Regimen Used\nPost-Transplant"
    ),
    expand = c(.02, .02)
  ) +
  scale_fill_manual(
    labels = \(x) gsub("_2", "", x),
    values = color_palette, name = "Post-Transplant\nDrug Class"
  ) +
  theme_minimal() +
  theme(
    plot.title = element_text(
      face = "bold", size = 16, hjust = 0.5,
      margin = margin(b = 10),
      family = "Helvetica Neue"
    ),
    plot.subtitle = element_text(
      size = 12, hjust = 0.5,
      margin = margin(b = 20),
      family = "Helvetica Neue"
    ),
    axis.title = element_blank(),
    axis.text = element_text(size = 11, color = "#333333", family = "Helvetica Neue"),
    axis.text.y = element_blank(),
    legend.position = "bottom",
    legend.title = element_text(size = 11, face = "bold", family = "Helvetica Neue"),
    legend.text = element_text(size = 10, family = "Helvetica Neue"),
    panel.grid = element_blank(),
    panel.border = element_blank(),
    plot.margin = margin(20, 20, 20, 20)
  )

Мы можем изменить форму данных, поместить обе оси в один столбец и применить соответствующий порядок/уровень факторов.

library(ggalluvial)
library(dplyr)

melted_top_transitions <- top_transitions %>% 
  tibble::rowid_to_column("ID") %>% 
  tidyr::pivot_longer(-c(ID, N)) %>% 
  mutate(value = factor(value, 
          levels = unique(c(levels(top_transitions$post_transplant_drug),
                            levels(top_transitions$last_pre_tx_drug))))) %>% 
  mutate(fclr = last(value), .by = ID)

Затем вам также необходимо изменить свой aes и предоставить:

Parameters `x`, `stratum`, and `alluvium` are required for data in lodes form

Я также использовал geom_flow вместо geom_alluvium (с последним почему-то не сработало). И чтобы «ширина линии» соответствовала N, нам нужно предоставить y для aes (ранее weight).

ggplot(melted_top_transitions, 
       aes(x = name, y = N,
           stratum = value, alluvium = ID,
           label = value)) +
  geom_flow(aes(fill = fclr), 
                width = 1/25, knot.pos = 0.1, curve_type = "sigmoid") +
  geom_stratum(width = 1/5, fill = "#F0F0F0", color = "#808080") +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), 
            size = 3, color = "#333333",
            family = "Helvetica Neue", fontface = "bold", 
            hjust = 0.5, vjust = 0.5) +
  scale_x_discrete(limits = c("last_pre_tx_drug", "post_transplant_drug"),
                   labels = c("Last Regimen Used\nPre-Transplant",
                              "First Regimen Used\nPost-Transplant"),
                   expand = c(.02, .02)) +
  scale_fill_manual(values = color_palette, name = "Post-Transplant\nDrug Class") +
  theme_minimal() +
  theme(plot.title = element_text(face = "bold", size = 16, hjust = 0.5, 
                                  margin = margin(b = 10), 
                                  family = "Helvetica Neue"),
        plot.subtitle = element_text(size = 12, hjust = 0.5, 
                                     margin = margin(b = 20), 
                                     family = "Helvetica Neue"),
        axis.title = element_blank(),
        axis.text = element_text(size = 11, color = "#333333", family = "Helvetica Neue"),
        axis.text.y = element_blank(),
        legend.position = "bottom",
        legend.title = element_text(size = 11, face = "bold", family = "Helvetica Neue"),
        legend.text = element_text(size = 10, family = "Helvetica Neue"),
        panel.grid = element_blank(),
        panel.border = element_blank(),
        plot.margin = margin(20, 20, 20, 20)) +
  scale_y_discrete()