Fig. 2.

Alignment of simulated datasets. (a) Simulation 1 and (b) Simulation 2: Visualizations of Dataset 1 (upper left panel) and Dataset 2 (lower left panel), separately using t-SNE before alignment; branches with points in the same colors are matched between datasets; visualization of the common embedding space of the two aligned datasets by MMD-MA (upper middle panel: points are colored according to their corresponding datasets; lower middle panel: points are colored according to their corresponding branches) and UnionCom (upper right panel: points are colored according to their corresponding datasets; lower right panel: points are colored according to their corresponding branches). The green branch of Dataset 2 of Simulation 2 (lower left panel of (b)) is a dataset-specific cell type, which has unique topological structure with branches of Dataset 2. (c) Averaged percentage of Neighborhood Overlap at different size of neighborhood (left panel: Simulation 1; right panel: Simulation 2)