Topic
UMAP misreading
Can I interpret distances, cluster sizes or trajectories from a UMAP?
UMAP preserves local neighborhoods and destroys global geometry: distances between islands, island size and the direction of a smear mean nothing reliable. The plot is a map for navigation, not evidence; conclusions must come from the high-dimensional data and a test.
- Why Your UMAP Is Misleading You in Spatial Transcriptomics
UMAP islands, cluster sizes and arcs are optical illusions in spatial data; the tissue coordinates and a permutation test are the only evidence that counts.