scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
, Distributions of eight summary statistics in the test data and the synthetic data generated by scDesign3 using cell type labels and spatial locations , respectively. Each number on top of a violin plot is the Kolmogorov-Smirnov distance between the synthetic data distribution and the test data distribution. A smaller number indicates better agreement between the synthetic data and the test data in terms of that summary statistic’s distribution.
Pearson’s correlation coefficientmeasures the similarity between two correlation matrices, one from the test data and the other from the synthetic data., PCA visualization of the real data and the synthetic data generated by scDesign3-ideal and scDesign3-spatial. Cell types are labeled by colors. Since the scDesgin3-spatial dataset was based on spatial locations only, it did not contain cell types.
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