Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-data-visualization-upset-plots

Maintainer FreedomIntelligence · Last updated April 1, 2026

UpSet plots for multi-set intersection visualization.

OpenClawNanoClawAnalysisWritingbio-data-visualization-upset-plots🧠 bioos extended suitebioos extended bioinformatics suiteupset

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-data-visualization-upset-plots

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

upset(fromExpression(data), order.by = 'freq', nsets = 6).
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).

Source Doc

Excerpt From SKILL.md

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')


## 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)
      ))

Use cases

Use bio-data-visualization-upset-plots to prepare publication-quality figures.
Apply bio-data-visualization-upset-plots when results need clear visual communication.