The accuracy of the number of clusters estimated by different methods on the twelve gold/silver standard datasets.

(A-D) The Pearson correlation between the estimated number of clusters and the ground-truth (Reference) across different methods: Secuer: based on the community detection on the anchor graph (A), Secuer-eigen: based on the eigenvalues of bipartite graph Laplacian between cells and anchors (B) (see Materials and Methods), Louvain (C), and Leiden (D). The mean absolute error (MSE) for each method is shown in the top left corner of the plot. (TIF)