Clustering and visualization of single-cell RNA-seq data using path metrics
Fig 4
Comparison of cluster structure preservation on PCA, UMAP and t-SNE embeddings.
Top row: 2d PCA, PM2, UMAP, and t-SNE embeddings of Cell Mix data set, colored by true cell type. Bottom row: average linkage dendrograms of cluster means for the rd embeddings, where r = 40 for PCA, r = 4 for PM2 and UMAP, and r = 3 for t-SNE.