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 Single-Cell ATAC-seq
The islands, the gaps between them, and the smear you're calling a trajectory are navigation aids, not measurements, so treat them that way before you write the discussion section.
- Why Your UMAP Is Misleading You in Single-Cell RNA-seq
Distances between islands, island size and the direction of a smear on your UMAP are artifacts of the embedding, and here is how to test each claim before it reaches a figure legend.
- 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.