Fig. 4: Original t-SNE embeddings and t-SNE embeddings optimized by scDEED on the CAR-T dataset. | Nature Communications

Fig. 4: Original t-SNE embeddings and t-SNE embeddings optimized by scDEED on the CAR-T dataset.

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

Fig. 4

a t-SNE plot of the CAR-T dataset at the study’s original perplexity 30. Dubious embeddings (b) and trustworthy embeddings (c) defined by scDEED at the original perplexity 30. d t-SNE plot of the CAR-T dataset at the perplexity 750 optimized by scDEED. Dubious embeddings (e) and trustworthy embeddings (f) defined by scDEED at the optimized perplexity 750.

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