The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense.
bioRxiv
; 2024 Jul 31.
Article
em En
| MEDLINE
| ID: mdl-38585748
ABSTRACT
A recent paper in PLOS Computational Biology (Chari and Pachter, 2023) claimed that t -SNE and UMAP embeddings of single-cell datasets fail to capture true biological structure. The authors argued that such embeddings are as arbitrary and as misleading as forcing the data into an elephant shape. Here we show that this conclusion was based on inadequate and limited metrics of embedding quality. More appropriate metrics quantifying neighborhood and class preservation reveal the elephant in the room while t -SNE and UMAP embeddings of single-cell data do not preserve high-dimensional distances, they can nevertheless provide biologically relevant information.
Texto completo:
1
Base de dados:
MEDLINE
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article