Plotting wompwomp Results with ggalluvial

library(dplyr)
library(ggplot2)
library(ggalluvial)
library(wompwomp)
set.seed(43)

df <- data.frame(
  tissue = c(
    "BRAIN", "BRAIN", "BRAIN",
    "STOMACH", "STOMACH", "STOMACH", "STOMACH", "STOMACH", "STOMACH",
    "HEART", "HEART", "HEART", "HEART", "HEART", "HEART", "HEART",
    "T CELL", "T CELL",
    "B CELL", "B CELL", "B CELL", "B CELL", "B CELL", "B CELL", "B CELL", "B CELL", "B CELL"
  ),
  cluster = c(
    1, 1, 2,
    1, 2, 2, 2, 2, 2,
    1, 3, 3, 3, 3, 3, 3,
    4, 4,
    4, 4, 4, 4, 4, 4, 4, 4, 4
  )
)

# preprocess (manual) and plot — unsorted + uncolored
df |> 
  dplyr::group_by(tissue, cluster) |> 
  dplyr::summarize(value = dplyr::n()) |> 
  dplyr::ungroup() |> 
  dplyr::mutate(dplyr::across(c(tissue, cluster), as.character)) |> 
  print() -> clus_df_gather

## `summarise()` has regrouped the output.
## ℹ Summaries were computed grouped by tissue and cluster.
## ℹ Output is grouped by tissue.
## ℹ Use `summarise(.groups = "drop_last")` to silence this message.
## ℹ Use `summarise(.by = c(tissue, cluster))` for per-operation grouping
##   (`?dplyr::dplyr_by`) instead.

## # A tibble: 8 × 3
##   tissue  cluster value
##   <chr>   <chr>   <int>
## 1 B CELL  4           9
## 2 BRAIN   1           2
## 3 BRAIN   2           1
## 4 HEART   1           1
## 5 HEART   3           6
## 6 STOMACH 1           1
## 7 STOMACH 2           5
## 8 T CELL  4           2

# unsorted plot
clus_df_gather |> 
  ggplot(aes(y = value, axis1 = tissue, axis2 = cluster)) +
  # alluvia color is column1
  geom_alluvium(aes(fill = tissue), width = 1/12) +
  geom_stratum(aes(fill = after_stat(stratum)), width = 1/12, color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(
    limits = c("tissue", "cluster"),
    expand = c(.05, .05)
  )

# sort (tidy) and plot - sorted + uncolored
clus_df_gather |> 
  sort_to_uncross(cols = c("tissue", "cluster"), wt = "value", options = list(weighted_metric = TRUE)) |> 
  print() -> clus_df_gather_sort

## # A tibble: 8 × 3
##   tissue  cluster value
##   <fct>   <fct>   <int>
## 1 B CELL  4           9
## 2 BRAIN   1           2
## 3 BRAIN   2           1
## 4 HEART   1           1
## 5 HEART   3           6
## 6 STOMACH 1           1
## 7 STOMACH 2           5
## 8 T CELL  4           2

clus_df_gather_sort |> 
  ggplot(aes(y = value, axis1 = tissue, axis2 = cluster)) +
  # alluvia color is column1
  geom_alluvium(aes(fill = tissue), width = 1/12) +
  geom_stratum(aes(fill = after_stat(stratum)), width = 1/12, color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(
    limits = c("tissue", "cluster"),
    expand = c(.05, .05)
  )

# color (tidy) and plot - sorted + colored
clus_df_gather_sort |> 
  get_lode_clusters(cols = c(tissue, cluster), wt = value) |> 
  print() -> cluster_mapping

## $cluster
## $cluster$`4`
## [1] 1
## 
## $cluster$`1`
## [1] 2
## 
## $cluster$`2`
## [1] 2
## 
## $cluster$`3`
## [1] 3
## 
## 
## $tissue
## $tissue$`B CELL`
## [1] 1
## 
## $tissue$BRAIN
## [1] 2
## 
## $tissue$HEART
## [1] 3
## 
## $tissue$STOMACH
## [1] 2
## 
## $tissue$`T CELL`
## [1] 1

clus_df_gather_sort |> 
  ggplot(aes(y = value, axis1 = tissue, axis2 = cluster)) +
  # alluvia color is column1
  geom_alluvium(aes(fill = tissue), width = 1/12) +
  geom_stratum(aes(fill = after_stat(stratum)), width = 1/12, color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(
    limits = c("tissue", "cluster"),
    expand = c(.05, .05)
  ) +
  scale_fill_manual(values = lode_cluster_pal(data = clus_df_gather_sort, cols = c(tissue, cluster), mapping = cluster_mapping))

crossing_edges_out <- compute_crossing_objective(clus_df_gather_sort, cols = c("tissue", "cluster"), wt = "value")
print(crossing_edges_out$output_objective)

## [1] 1

Calling wompwomp from inside ggalluvial

Everything above sorts and colours the data frame first and plots the result. Development versions of ggalluvial can instead call wompwomp from within the alluvial layers themselves, through the sort_strata and color_strata parameters of stat_stratum(), stat_alluvium() and stat_flow(). See vignette("ggalluvial_integration").

sessionInfo()

## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] wompwomp_1.0.0    ggalluvial_0.12.6 ggplot2_4.0.3     dplyr_1.2.1      
## [5] rmarkdown_2.32   
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6       jsonlite_2.0.0     compiler_4.6.1     Rcpp_1.1.2        
##  [5] tidyselect_1.2.1   stringr_1.6.0      tidyr_1.3.2        jquerylib_0.1.4   
##  [9] scales_1.4.0       yaml_2.3.12        fastmap_1.2.0      R6_2.6.1          
## [13] labeling_0.4.3     generics_0.1.4     igraph_2.3.4       knitr_1.52        
## [17] MASS_7.3-66        polyclip_1.10-7    tibble_3.3.1       maketools_1.3.2   
## [21] bslib_0.12.0       pillar_1.11.1      RColorBrewer_1.1-3 rlang_1.3.0       
## [25] utf8_1.2.6         stringi_1.8.9      cachem_1.1.0       xfun_0.62         
## [29] sass_0.4.10        sys_3.4.3          S7_0.2.2           otel_0.2.0        
## [33] cli_3.6.6          tweenr_2.0.3       withr_3.0.3        magrittr_2.0.5    
## [37] digest_0.6.39      grid_4.6.1         ggforce_0.5.0      lifecycle_1.0.5   
## [41] vctrs_0.7.3        evaluate_1.0.5     glue_1.8.1         farver_2.1.2      
## [45] buildtools_1.0.0   purrr_1.2.2        tools_4.6.1        pkgconfig_2.0.3   
## [49] htmltools_0.5.9

- Calling wompwomp from inside ggalluvial