003 Name Skill 3e0757ba

---
name: bio-data-visualization-upset-plots
description: Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets.
tool_type: mixed
primary_tool: UpSetR
---

## Version Compatibility

Reference examples tested with: matplotlib 3.8+, pandas 2.2+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.

# UpSet Plots

**"Visualize set intersections"** → Replace Venn diagrams with UpSet plots for comparing overlaps across many gene/peak/variant sets.
- R: `UpSetR::upset(fromList(sets))`
- Python: `upsetplot.UpSet.from_memberships()` or `from_indicators()`

## UpSetR (R) - Basic Plot

```r
library(UpSetR)

# From binary matrix (rows = elements, columns = sets)
upset(fromExpression(data), order.by = 'freq', nsets = 6)

# From list of sets
gene_sets <- list(
    SetA = c('Gene1', 'Gene2', 'Gene3', 'Gene4'),
    SetB = c('Gene2', 'Gene3', 'Gene5', 'Gene6'),
    SetC = c('Gene1', 'Gene3', 'Gene6', 'Gene7'),
    SetD = c('Gene3', 'Gene4', 'Gene7', 'Gene8')
)
upset(fromList(gene_sets), order.by = 'freq', nsets = 4)
```

## UpSetR Customization

```r
# Customized appearance
upset(fromList(gene_sets),
      nsets = 6,
      nintersects = 40,
      order.by = 'freq',
      decreasing = TRUE,
      mb.ratio = c(0.6, 0.4),  # Matrix to bar ratio
      point.size = 3,
      line.size = 1.5,
      mainbar.y.label = 'Intersection Size',
      sets.x.label = 'Set Size',
      text.scale = c(1.5, 1.3, 1.3, 1, 1.5, 1.3),
      set_size.show = TRUE,
      set_size.scale_max = 500)

# Custom set colors
upset(fromList(gene_sets),
      sets.bar.color = c('#E64B35', '#4DBBD5', '#00A087', '#3C5488'),
      main.bar.color = '#7E6148',
      matrix.color = '#7E6148')
```

## UpSetR with Queries

**Goal:** Highlight specific set intersections of interest within an UpSet plot.

**Approach:** Define query lists specifying which set combinations to highlight, assigning each a distinct color, so they stand out against the default bars.

```r
# Highlight specific intersections
upset(fromList(gene_sets),
      order.by = 'freq',
      queries = list(
          list(query = intersects,
               params = list('SetA', 'SetB'),
               color = '#E64B35',
               active = TRUE),
          list(query = intersects,
               params = list('SetA', 'SetC', 'SetD'),
               color = '#4DBBD5',
               active = TRUE)
      ))

# Highlight elements matching criteria
# Requires attribute data frame with element names as row names
upset(fromList(gene_sets),
      queries = list(
          list(query = elements,
               params = list('logFC', 1, 2),  # column, min, max
               color = 'red',
               active = TRUE)
      ))
```

## UpSetR with Metadata Boxplots

```r
# Add attribute plots below intersection matrix
# Requires data frame with set membership columns + attribute columns
upset(data,
      order.by = 'freq',
      boxplot.summary = c('logFC', 'pvalue'))

# Custom attribute plots
upset(data,
      order.by = 'freq',
      attribute.plots = list(
          gridrows = 50,
          plots = list(
              list(plot = histogram, x = 'logFC', queries = FALSE),
              list(plot = scatter_plot, x = 'logFC', y = 'pvalue', queries = TRUE)
          ),
          ncols = 2
      ))
```

## upsetplot (Python) - Basic

```python
from upsetplot import from_memberships, plot, UpSet
import matplotlib.pyplot as plt

# From membership lists
memberships = [
    ['SetA', 'SetB'],
    ['SetA'],
    ['SetB', 'SetC'],
    ['SetA', 'SetB', 'SetC'],
    ['SetC'],
    ['SetA', 'SetC']
]
data = from_memberships(memberships)

# Basic plot
plot(data, show_counts=True)
plt.savefig('upset.png', dpi=150, bbox_inches='tight')
```

## upsetplot from DataFrame

```python
import pandas as pd
from upsetplot import from_contents, UpSet

# From dict of sets
gene_sets = {
    'SetA': ['Gene1', 'Gene2', 'Gene3', 'Gene4'],
    'SetB': ['Gene2', 'Gene3', 'Gene5', 'Gene6'],
    'SetC': ['Gene1', 'Gene3', 'Gene6', 'Gene7']
}
data = from_contents(gene_sets)

upset = UpSet(data, subset_size='count', show_counts=True, sort_by='cardinality')
upset.plot()
plt.savefig('upset.png', dpi=150, bbox_inches='tight')
```

## upsetplot Customization

```python
from upsetplot import UpSet

upset = UpSet(data,
              subset_size='count',
              show_counts=True,
              show_percentages=True,
              sort_by='cardinality',  # or 'degree'
              sort_categories_by='cardinality',
              facecolor='#4DBBD5',
              element_size=40,
              intersection_plot_elements=10)

fig = plt.figure(figsize=(12, 8))
upset.plot(fig=fig)
```

## upsetplot with Metadata

```python
# Add data attributes for additional plots
df = pd.DataFrame({
    'SetA': [True, True, False, True, False],
    'SetB': [True, False, True, True, False],
    'SetC': [False, True, True, False, True],
    'logFC': [1.2, -0.8, 2.1, 0.5, -1.5],
    'pvalue': [0.01, 0.05, 0.001, 0.2, 0.03]
})
df = df.set_index(['SetA', 'SetB', 'SetC'])

upset = UpSet(df, subset_size='count')
upset.add_stacked_bars(by='significant', colors=['gray', 'red'])
# Or: upset.add_catplot(value='logFC', kind='box')
upset.plot()
```

## Save UpSet Plots

```r
# R - to PDF
pdf('upset_plot.pdf', width = 10, height = 6)
upset(fromList(gene_sets), order.by = 'freq')
dev.off()

# R - to PNG
png('upset_plot.png', width = 10, height = 6, units = 'in', res = 300)
upset(fromList(gene_sets), order.by = 'freq')
dev.off()
```

```python
# Python
fig = plt.figure(figsize=(10, 6))
upset.plot(fig=fig)
plt.savefig('upset.pdf', bbox_inches='tight')
plt.savefig('upset.png', dpi=300, bbox_inches='tight')
```

## Related Skills

- data-visualization/heatmaps-clustering - Alternative for smaller sets
- pathway-analysis/enrichment-visualization - Gene set overlaps
- differential-expression/de-results - DE gene set comparisons