Fig. 3: Cell embedding benchmark in gold-standard scRNA-surface protein and scRNA-scATAC datasets.

a Schematic representation of the benchmarking process; b Purity, Transfer accuracy, Connectivity, and FOSCTTM scores for the six benchmarked methods (scConfluence, Seurat, Liger, MultiMAP, Uniport, and scGLUE) in two scRNA-scATAC datasets profiled from PBMC and bone marrow. Error bars in the plots specify the standard deviation across n = 5 random initialization seeds for each method and they are centered on the median result. Inside bar plots, small dark stars represent individual seed results. Source data are provided as a Source Data file; c UMAP visualizations of scConfluence’s cell embeddings in the same datasets as (b). Cells are colored based on their modality of origin, their cell type annotation, or their batch of origin (when multiple batches are present in the data), respectively; d Same scores and methods as (b), but computed on the two scRNA-surface protein datasets of the benchmark profiled from bone marrow. Error bars in the plots specify the standard deviation across n = 5 random initialization seeds for each method and they are centered on the median result. Inside bar plots, small dark stars represent individual seed results. Source data are provided as a Source Data file.; e UMAP visualizations of scConfluence’s cell embeddings on the two scRNA-surface protein datasets with cells colored according to the same rules as (c).