Fig. 3
From: Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Performance of five DR pipelines (scran, Seurat, ZinbWave, DCA, and scVI) with default parameters and a dimension of 10 (legend “default”) or after parameter optimization (legend “best”) on our benchmark of ten datasets. a AMI (left) and silhouette (right) reached by each method on each dataset. b UMAP representation of Zhengmix8eq after DR by each method (in column) using default parameters (top two rows) of after parameter optimization (bottom two rows). In each row, cells are colored either based on their true cell type (rows 1 and 3) or based on a k-means clustering