Skill: Sankey Bubble plot (R)

Category

Omics

When to Use

Create a Sankey Bubble plot visualization in R for biomedical data analysis and research publications.

Required R Packages

• ggalluvial
• patchwork
• readr
• tidyverse

Minimal Reproducible Code

# Load packages
library(ggalluvial)
library(patchwork)
library(readr)
library(tidyverse)

# Prepare data
# Load data
data <- read_tsv("files/DAVID.txt")

# Add a new categorical column
get_category <- function(cat) {
  if (grepl("BP", cat)) return("BP")
  if (grepl("MF", cat)) return("MF")
  if (grepl("CC", cat)) return("CC")
  if (grepl("KEGG", cat)) return("KEGG")
  return(NA)
}
data$MainCategory <- sapply(data$Category, get_category)

# Remove SMART and NA
data2 <- data %>%
  filter(!grepl("SMART", Category)) %>%
  filter(!is.na(MainCategory))

# Sort each category and take the top 10
topN <- function(data, n=10) {
  data %>%
  arrange(desc(Count), PValue) %>%
  head(n)
}
result <- data2 %>%
  group_by(MainCategory) %>%
  group_modify(~topN(.x, 10)) %>%
  ungroup()

# KEGG pathway annotation
result <- result %>%
  mutate(
    Source = ifelse(MainCategory == "KEGG", "KEGG", "GO"),
    KEGG_Group = case_when(
      MainCategory == "KEGG" & str_detect(Term,"Neuro|synapse|neurodegeneration|Alzheimer|Parkinson|Prion") ~ "Nervous system",
      MainCategory == "KEGG" & str_detect(Term, "Cytokine|inflammatory") ~ "Immune system",
      MainCategory == "KEGG" & str_detect(Term, "Lipid|atherosclerosis") ~ "Lipid metabolism",
      MainCategory == "KEGG" ~ "Other KEGG",
      TRUE ~ NA_character_
      ),
    GO_Group = ifelse(MainCategory != "KEGG", MainCategory, NA)
    )
alluvial_data <- result %>%
# ... (see full tutorial for more)

Key Parameters

• y: Maps 1 to the y aesthetic
• fill: Maps Group to the fill aesthetic
• x: Maps min to the x aesthetic
• size: Maps Count to the size aesthetic
• alpha: Controls transparency (0 = fully transparent, 1 = opaque)
• width: Controls element width
• position: Position adjustment (identity, dodge, stack, fill)
• stat: Statistical transformation to use

Tips

• Use theme_minimal() or theme_bw() for clean, publication-ready plots
• Customize color scales with scale_fill_manual() or scale_color_brewer()
• Include appropriate statistical thresholds (e.g., FDR < 0.05, |log2FC| > 1) in the visualization

Full Tutorial

https://openbiox.github.io/Bizard/Omics/SankeyBubblePlot.html