Fig. 8: Original UMAP embeddings and UMAP embeddings optimized by scDEED on the Samusik dataset. | Nature Communications

Fig. 8: Original UMAP embeddings and UMAP embeddings optimized by scDEED on the Samusik dataset.

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

Fig. 8

a UMAP plot of the Samusik dataset at the study’s original hyperparameters, min.dist = 0.2 and n.neighbors = 15. Dubious embeddings (b) and trustworthy embeddings (c) defined by scDEED at the original hyperparameters. d UMAP plot of the Samusik dataset with the hyperparameters jointly optimized by scDEED, min.dist = 0.7 and n.neighbors = 160. Dubious embeddings (e) and trustworthy embeddings (f) defined by scDEED at the optimized hyperparameters.

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