Fig. 3. The Comparison between DESC and scVI when batch information was not provided in the analysis of macaque retina data.

a The t-SNE results of DESC when no batch information provided and the cells are colored by cell type, macaque id, region id, and sample id, respectively; b scVI when batch information was not provided and cells are colored by cell type, macaque id, region id, and sample id, respectively. The cells are mixed well by macaque id, region, and sample id in DESC, but are completely separated by macaque id, region, and sample id in scVI. These results indicate that DESC is able to remove complex batch effect without explicit use of batch information.