KNOWLEDGE GUIDE · REVIEWED 01 SEP 2026
What a single-cell UMAP can—and cannot—show
UMAP compresses high-dimensional cellular measurements into two dimensions while trying to preserve useful local neighbourhood structure.
01Read neighbourhoods cautiously
Nearby cells often have similar profiles, but the visual distance between remote clusters is not a calibrated biological measurement.
02Annotations are interpretations
Cluster labels usually combine marker genes, references and expert judgement. Automated labels should remain traceable and open to correction.
03Check the upstream choices
Filtering, normalisation, feature selection, integration and UMAP parameters all influence the final map.
