Extended Data Fig. 2: Robustness of the clustering.

a) UMAP projection of the 654 plaque samples based on RNA-seq dataset. The color indicates the cluster corresponding to the plaque type cluster from the SNN modularity optimization-based clustering algorithm after batch and hospital correction. b) Heatmap depicts relative gene expression levels of selected plaque type enriched genes in individual samples and plaque clusters. c) Correspondence of clusters derived from batch corrected and original dataset. Numbers indicate sample counts in the intersection of the corresponding clusters. d) UMAP projection of the 654 plaque samples based on RNA-seq dataset. The color indicates the cluster corresponding to the plaque type cluster from the SNN modularity optimization-based clustering algorithm after batch and hospital correction using Harmony integration. e) Heatmap depicts relative gene expression levels of selected plaque type enriched genes in individual samples and plaque clusters. f) Correspondence of clusters derived from batch corrected (using Harmony) and original dataset. Numbers indicate sample counts in the intersection of the corresponding clusters. g) UMAP projection of the 654 plaque samples based on RNA-seq dataset. The color indicates the frequency of the sample being assigned in other than the original cluster in permutation analysis. h) Distribution of the frequencies of the sample being assigned in other than the original cluster in permutation analysis.