Fig. 4

Evaluation of integration performance at varying sequencing depth for multiome cells. A Details of the simulation scheme. B, C Performance of cell type annotation and peak-gene association recovery in the PBMC-based simulations (B) and BMMC-based simulations (C: left panel, 2000 multiome cells; right panel, 4000 multiome cells). ARI and NMI measures agreement between predicted cell type and ground-truth labels. Peak-gene pair % recovered is the percentage of peak-gene pairs correctly identified comparing to the ground-truth list calculated using 10,412 paired PBMC cells (B) and 6740 BMMC cells (C). F1 is the prediction accuracy normalized by the number of false positives and false negatives. D Performance of cell type annotation using Seurat v3 or Seurat v4 at increasing depth or increasing number of cells. E Performance of peak-gene association recovery using Seurat v3 or Seurat v4 at increasing depth or increasing number of cells. For all subplots, error bar is mean ± standard deviation