Cannot re-order axes in ggalluvial

I have read through all of the ggalluvial posts that I can find about ordering the axes in an alluvial diagram. Each of my axes is a factor variable and I have set the levels to be in the order I wish for them to appear in the plot. The first of my two axes is correctly ordered per the levels of its factor variable and the order changes as it should when I change the levels. However, the second axis does not reflect the levels of its underlying factor variable. For some reason the second axis appears to mirror the levels of the first axis for all overlapping drug classes and is not responsive to any changes I make to the levels.

Does any one have any suggestions for address this problem?

For refernece, here is my data:

top_transitions <- data.frame(
  last_pre_tx_drug = c("DPP4 inhibitors", "DPP4 inhibitors",
                       "Insulin", "Insulin", "Insulin", 
                       "None", "None", "None", "None", "None",
                       "Sulfonylureas", "Sulfonylureas", 
                       "Sulfonylureas", "Sulfonylureas"),

  post_transplant_drug = c("Insulin", "Insulin + DPP4 inhibitors", 
                           "Insulin", "None", "Insulin + GLP-1 RAs", 
                           "DPP4 inhibitors", "Insulin", "None", 
                           "Biguanides", "Sulfonylureas", 
                           "Insulin + Sulfonylureas", "Insulin", 
                           "None", "Sulfonylureas"),

  N = c(1809, 1005, 35053, 4506, 808, 2200, 12087, 36052, 
        1304, 3303, 1301, 5017, 1302, 1207)
)

top_transitions$last_pre_tx_drug <- factor(top_transitions$last_pre_tx_drug, 
      levels = c("DPP4 inhibitors", "Insulin", "None", "Sulfonylureas"))

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

And here is the code I'm using for my plot:

# Color palette based on the levels of post_transplant_drug
color_palette <- c(
  "DPP4 inhibitors" = "#4393C3",
  "Insulin + Sulfonylureas" = "#B2182B",
  "Insulin" = "#2166AC",
  "Insulin + DPP4 inhibitors" = "#A6A6A6",
  "None" = "#92C5DE",
  "Insulin + GLP-1 RAs" = "#1B7837",
  "Biguanides" = "#F4A582",
  "Sulfonylureas" = "#D6604D"
)

library(ggalluvial)

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(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(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))

No matter what I try, the right most axis always appears as follows:

Solution

We can reshape the data and put both axes in the same column and apply the appropriate factor order/level.

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)

Then, you also need to change your aes and provide:

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

I also used geom_flow instead of geom_alluvium (for some reason it didn't work with the latter). And to get the "linewidth" to correspond to N we need to provide y to aes (previously 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()