Fig. 2

Benchmarking scREG with other dimension reduction Methods. A, B Scatter plots visualize the silhouette index (SI) of following methods versus scREG: PCA for RNA data, LSA for ATAC data, concatenation of top PCs of RNA and top factors of ATAC, scAI, MOFA+, and intNMF, which differ from scREG by lacking the cis-regulatory potential term. Each dot represents the SI of one cell. Each scatter plot compare scREG with another dimension reduction method. Y axis represent the SI from scREG and X-axes represent that from alternative methods. SI represents the similarity of each cell with the cells in same cell type compared to those from other cell types. The percentage of cells with higher SI in scREG is labeled top of the figures. Color of dots represent true label of cells as shown in Fig. 3B. C Comparison of SI values from 7 different methods in some cell types. cells achieve higher SI values when using scREG