Figure 3.

CLEAR corrects batch effects effectively. (A) Upper panel: UMAP visualization showing different methods’ performance on integrating DoubleNeg and pDC cells from two batches. Bottom panel: UMAP visualization showing different methods’ performance on separating four cell types. Notice that CLEAR’s representations also preserve the biological similarity between CD141 cells and CD1C cells. (B) The quantitative performance of different methods on batch effect removal, measured by ARI and ASW.