Fig. 2: Original t-SNE embeddings and t-SNE embeddings optimized by scDEED on the Hydra dataset. | Nature Communications

Fig. 2: Original t-SNE embeddings and t-SNE embeddings optimized by scDEED on the Hydra dataset.

From: Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters

Fig. 2

a t-SNE plot of the Hydra dataset at the perplexity 40 used in the original study. b–c Dubious cell embeddings (b) and trustworthy cell embeddings (c) defined by scDEED at the perplexity 40. d t-SNE plot of the Hydra dataset at the perplexity 230 optimized by scDEED. e–f Dubious cell embeddings (e) and trustworthy cell embeddings (f) defined by scDEED at the perplexity 230.

Back to article page