bio-data-visualization-flow-and-transition-plots

Installation
SKILL.md

Version Compatibility

Reference examples tested with: ggalluvial 0.12+, networkD3 0.4+, plotly 4.10+, consort 0.2+ (CONSORT diagrams), pySankey 0.0.1+.

Before using code patterns, verify installed versions match. If versions differ:

  • R: packageVersion('<pkg>') then ?function_name
  • Python: pip show <package> then help(module.function)

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

Flow and Transition Plots

"Show how things flow between categories" -> Render entities as ribbons whose width encodes count, flowing between ordered columns of categories. Sankey emphasizes total flow magnitude; alluvial emphasizes per-entity continuity (each row's path is traceable); CONSORT formalizes the trial-filtering convention. The decision space: which method (Sankey vs alluvial vs CONSORT), how to order categories within each column, and whether to highlight specific entity trajectories.

  • R: ggalluvial::geom_alluvium, networkD3::sankeyNetwork, consort::consort_plot
  • Python: plotly.graph_objects.Sankey, pySankey

The Single Most Important Modern Insight -- Sankey vs Alluvial Are Different

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