Alluvial diagram with varying aesthetic / colors over one flow in R based on ggplot2

Question

I have created the following alluvial diagram in R as follows:

df <- data.frame(Variable = c("X1", "X2", "X3", "X4", "X5", "X6"),
                 Pearson1 = c(6, 3, 2, 5, 4, 1),
                 Spearman1 = c(6, 5, 1, 2, 3, 4),
                 Kendall1 = c(6, 5, 1, 2, 3, 4),
                 Pearson2 = c(6, 5, 1, 2, 3, 4),
                 Spearman2 = c(6, 5, 1, 2, 4, 3),
                 Kendall2 = c(6, 5, 1, 2, 3, 4))
df$freq<-1
alluvial(df[1:7], freq=df$freq, cex = 0.7,col= "red")

which results in

How can I set some specific lines to have different col than red? e.g. X1 from Variables to Pearson1, and then again from Kendall1 to Spearman2 and X3 in all states? I see I can't do that based on alluvial(). How can I recreate the above alluvial based on another function??

Answer 1

ggalluvial allows for varying aesthetics over one "flow" (or alluvium). The documentation provides a trick to use geom_flow with stat = "alluvium" and to specify "lode.guidance = "frontback".

The actual aesthetic (color) will need to be added to the data. geom_flow and geom_stratum will require different columns for the aesthetic, (try what happens when you use the same for both). I am passing the color directly and using scale_identity, but you can of course also use random values and then define your colors with scale_manual.

library(ggalluvial)
#> Loading required package: ggplot2
library(tidyverse)
df <- data.frame(Variable = c("X1", "X2", "X3", "X4", "X5", "X6"),
                 Pearson1 = c(6, 3, 2, 5, 4, 1),
                 Spearman1 = c(6, 5, 1, 2, 3, 4),
                 Kendall1 = c(6, 5, 1, 2, 3, 4),
                 Pearson2 = c(6, 5, 1, 2, 3, 4),
                 Spearman2 = c(6, 5, 1, 2, 4, 3),
                 Kendall2 = c(6, 5, 1, 2, 3, 4))

df_long <-
  df %>%
  ## reshape your data in order to bring it to the right shape
  mutate(across(everything(), as.character)) %>%
  rownames_to_column("ID") %>%
  pivot_longer(-ID) %>%
  ## correct order of your x
  mutate(
    name = factor(name, levels = names(df)),
    ## now hard code where you want to change the color.
    ## lodes need a different highlighting then your strata
    ## there are of course many ways to add this information, I am using case_when here
    ## you could also create separate vectors and add them to your data frame
    highlight_lode = case_when(
      ID == 3 ~ "blue",
      ID == 1 & name %in% c("Variable", "Kendall1", "Pearson2") ~ "orange",
      TRUE ~ "red"
    ),
    highlight_stratum = case_when(
      ID == 3 ~ "blue",
      ID == 1 & name %in% c(
        "Variable", "Pearson1", "Kendall1", "Pearson2",
        "Spearman2"
      ) ~ "orange",
      TRUE ~ "red"
    )
  )

ggplot(df_long, 
       ## now use different color aesthetics in geom_flow and geom_stratum
       aes(x = name, stratum = value, alluvium = ID, label = value)) +
  ## I took this trick with lode guidance from the documentation - this allows varying aesthetics over one flow. 
  geom_flow(aes(fill = highlight_lode), stat = "alluvium", lode.guidance = "frontback", color = "darkgray") +
  geom_stratum(aes(fill = highlight_stratum)) +
  geom_text(stat = "stratum") +
  ## as I have named the colors directly, it is appropriate to use scale_identity
  scale_fill_identity()
#> Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.

^{Created on 2023-01-29 with reprex v2.0.2}